Starting phenix.real_space_refine on Wed Apr 17 04:48:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4i_17409/04_2024/8p4i_17409.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4i_17409/04_2024/8p4i_17409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4i_17409/04_2024/8p4i_17409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4i_17409/04_2024/8p4i_17409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4i_17409/04_2024/8p4i_17409.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4i_17409/04_2024/8p4i_17409.pdb" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 289 5.16 5 C 27472 2.51 5 N 6970 2.21 5 O 8245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 94": "NH1" <-> "NH2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 138": "NH1" <-> "NH2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "F ARG 9": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 94": "NH1" <-> "NH2" Residue "F ARG 129": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F ARG 138": "NH1" <-> "NH2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F ARG 231": "NH1" <-> "NH2" Residue "F ARG 272": "NH1" <-> "NH2" Residue "G ARG 9": "NH1" <-> "NH2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 67": "NH1" <-> "NH2" Residue "G ARG 94": "NH1" <-> "NH2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G ARG 138": "NH1" <-> "NH2" Residue "G ARG 199": "NH1" <-> "NH2" Residue "G ARG 231": "NH1" <-> "NH2" Residue "G ARG 272": "NH1" <-> "NH2" Residue "H ARG 9": "NH1" <-> "NH2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H ARG 94": "NH1" <-> "NH2" Residue "H ARG 129": "NH1" <-> "NH2" Residue "H ARG 132": "NH1" <-> "NH2" Residue "H ARG 138": "NH1" <-> "NH2" Residue "H ARG 199": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 272": "NH1" <-> "NH2" Residue "I ARG 9": "NH1" <-> "NH2" Residue "I ARG 67": "NH1" <-> "NH2" Residue "I ARG 94": "NH1" <-> "NH2" Residue "I ARG 129": "NH1" <-> "NH2" Residue "I ARG 132": "NH1" <-> "NH2" Residue "I ARG 138": "NH1" <-> "NH2" Residue "I ARG 199": "NH1" <-> "NH2" Residue "I ARG 231": "NH1" <-> "NH2" Residue "I ARG 272": "NH1" <-> "NH2" Residue "J ARG 9": "NH1" <-> "NH2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 94": "NH1" <-> "NH2" Residue "J ARG 129": "NH1" <-> "NH2" Residue "J ARG 132": "NH1" <-> "NH2" Residue "J ARG 138": "NH1" <-> "NH2" Residue "J ARG 199": "NH1" <-> "NH2" Residue "J ARG 231": "NH1" <-> "NH2" Residue "J ARG 272": "NH1" <-> "NH2" Residue "K ARG 9": "NH1" <-> "NH2" Residue "K ARG 67": "NH1" <-> "NH2" Residue "K ARG 94": "NH1" <-> "NH2" Residue "K ARG 129": "NH1" <-> "NH2" Residue "K ARG 132": "NH1" <-> "NH2" Residue "K ARG 138": "NH1" <-> "NH2" Residue "K ARG 199": "NH1" <-> "NH2" Residue "K ARG 231": "NH1" <-> "NH2" Residue "K ARG 272": "NH1" <-> "NH2" Residue "L ARG 9": "NH1" <-> "NH2" Residue "L ARG 67": "NH1" <-> "NH2" Residue "L ARG 94": "NH1" <-> "NH2" Residue "L ARG 129": "NH1" <-> "NH2" Residue "L ARG 132": "NH1" <-> "NH2" Residue "L ARG 138": "NH1" <-> "NH2" Residue "L ARG 199": "NH1" <-> "NH2" Residue "L ARG 231": "NH1" <-> "NH2" Residue "L ARG 272": "NH1" <-> "NH2" Residue "M ARG 9": "NH1" <-> "NH2" Residue "M ARG 67": "NH1" <-> "NH2" Residue "M ARG 94": "NH1" <-> "NH2" Residue "M ARG 129": "NH1" <-> "NH2" Residue "M ARG 132": "NH1" <-> "NH2" Residue "M ARG 138": "NH1" <-> "NH2" Residue "M ARG 199": "NH1" <-> "NH2" Residue "M ARG 231": "NH1" <-> "NH2" Residue "M ARG 272": "NH1" <-> "NH2" Residue "N ARG 9": "NH1" <-> "NH2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "N ARG 94": "NH1" <-> "NH2" Residue "N PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 129": "NH1" <-> "NH2" Residue "N ARG 132": "NH1" <-> "NH2" Residue "N ARG 138": "NH1" <-> "NH2" Residue "N ARG 199": "NH1" <-> "NH2" Residue "N ARG 231": "NH1" <-> "NH2" Residue "N ARG 272": "NH1" <-> "NH2" Residue "O ARG 9": "NH1" <-> "NH2" Residue "O ARG 67": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 129": "NH1" <-> "NH2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "O ARG 138": "NH1" <-> "NH2" Residue "O ARG 199": "NH1" <-> "NH2" Residue "O ARG 231": "NH1" <-> "NH2" Residue "O ARG 272": "NH1" <-> "NH2" Residue "P ARG 9": "NH1" <-> "NH2" Residue "P ARG 67": "NH1" <-> "NH2" Residue "P ARG 94": "NH1" <-> "NH2" Residue "P ARG 129": "NH1" <-> "NH2" Residue "P ARG 132": "NH1" <-> "NH2" Residue "P ARG 138": "NH1" <-> "NH2" Residue "P ARG 199": "NH1" <-> "NH2" Residue "P ARG 231": "NH1" <-> "NH2" Residue "P ARG 272": "NH1" <-> "NH2" Residue "Q ARG 9": "NH1" <-> "NH2" Residue "Q ARG 67": "NH1" <-> "NH2" Residue "Q ARG 94": "NH1" <-> "NH2" Residue "Q ARG 129": "NH1" <-> "NH2" Residue "Q ARG 132": "NH1" <-> "NH2" Residue "Q ARG 138": "NH1" <-> "NH2" Residue "Q ARG 199": "NH1" <-> "NH2" Residue "Q ARG 231": "NH1" <-> "NH2" Residue "Q ARG 272": "NH1" <-> "NH2" Residue "R ARG 9": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "R ARG 94": "NH1" <-> "NH2" Residue "R ARG 129": "NH1" <-> "NH2" Residue "R ARG 132": "NH1" <-> "NH2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 199": "NH1" <-> "NH2" Residue "R ARG 231": "NH1" <-> "NH2" Residue "R ARG 272": "NH1" <-> "NH2" Residue "S ARG 9": "NH1" <-> "NH2" Residue "S TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 67": "NH1" <-> "NH2" Residue "S ARG 94": "NH1" <-> "NH2" Residue "S ARG 129": "NH1" <-> "NH2" Residue "S ARG 132": "NH1" <-> "NH2" Residue "S ARG 138": "NH1" <-> "NH2" Residue "S ARG 199": "NH1" <-> "NH2" Residue "S ARG 231": "NH1" <-> "NH2" Residue "S ARG 272": "NH1" <-> "NH2" Residue "U ARG 9": "NH1" <-> "NH2" Residue "U ARG 67": "NH1" <-> "NH2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "U ARG 129": "NH1" <-> "NH2" Residue "U ARG 132": "NH1" <-> "NH2" Residue "U ARG 138": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U ARG 231": "NH1" <-> "NH2" Residue "U ARG 272": "NH1" <-> "NH2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 42976 Number of models: 1 Model: "" Number of chains: 17 Chain: "B" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "D" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 299} Chain: "F" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "G" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "I" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 299} Chain: "J" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "K" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "L" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "M" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "N" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 299} Chain: "O" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "P" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 299} Chain: "Q" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "R" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "S" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "U" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Time building chain proxies: 21.51, per 1000 atoms: 0.50 Number of scatterers: 42976 At special positions: 0 Unit cell: (137.55, 139.65, 217.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 289 16.00 O 8245 8.00 N 6970 7.00 C 27472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.41 Conformation dependent library (CDL) restraints added in 7.8 seconds 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10132 Finding SS restraints... Secondary structure from input PDB file: 205 helices and 47 sheets defined 34.1% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'B' and resid 21 through 39 removed outlier: 4.119A pdb=" N GLU B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.826A pdb=" N ILE B 60 " --> pdb=" O TRP B 56 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY B 61 " --> pdb=" O PHE B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 61' Processing helix chain 'B' and resid 62 through 74 removed outlier: 3.713A pdb=" N THR B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE B 69 " --> pdb=" O TYR B 65 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 95 removed outlier: 3.657A pdb=" N GLN B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 169 through 178 removed outlier: 3.716A pdb=" N LEU B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 removed outlier: 3.502A pdb=" N ALA B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 203 " --> pdb=" O ARG B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 224 Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.703A pdb=" N PHE B 237 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 4.104A pdb=" N TYR B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 39 removed outlier: 3.983A pdb=" N ASN D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.801A pdb=" N ILE D 60 " --> pdb=" O TRP D 56 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY D 61 " --> pdb=" O PHE D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 61' Processing helix chain 'D' and resid 62 through 76 removed outlier: 3.633A pdb=" N THR D 66 " --> pdb=" O HIS D 62 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE D 69 " --> pdb=" O TYR D 65 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS D 75 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 removed outlier: 3.851A pdb=" N ILE D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 Processing helix chain 'D' and resid 165 through 168 Processing helix chain 'D' and resid 169 through 178 removed outlier: 3.664A pdb=" N LEU D 173 " --> pdb=" O VAL D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 206 removed outlier: 3.744A pdb=" N TYR D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.640A pdb=" N PHE D 237 " --> pdb=" O PHE D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 removed outlier: 4.501A pdb=" N TYR D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 37 Processing helix chain 'F' and resid 38 through 40 No H-bonds generated for 'chain 'F' and resid 38 through 40' Processing helix chain 'F' and resid 56 through 61 removed outlier: 3.695A pdb=" N ILE F 60 " --> pdb=" O TRP F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 75 removed outlier: 3.748A pdb=" N HIS F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU F 72 " --> pdb=" O LYS F 68 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS F 75 " --> pdb=" O HIS F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.755A pdb=" N GLN F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 140 Processing helix chain 'F' and resid 165 through 168 Processing helix chain 'F' and resid 169 through 178 removed outlier: 3.835A pdb=" N LEU F 173 " --> pdb=" O VAL F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 206 removed outlier: 3.709A pdb=" N SER F 198 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA F 202 " --> pdb=" O SER F 198 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE F 203 " --> pdb=" O ARG F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 225 removed outlier: 3.689A pdb=" N LYS F 221 " --> pdb=" O THR F 217 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N MET F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N CYS F 225 " --> pdb=" O LYS F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 235 Processing helix chain 'F' and resid 273 through 278 removed outlier: 3.593A pdb=" N LYS F 277 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR F 278 " --> pdb=" O ILE F 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 273 through 278' Processing helix chain 'G' and resid 21 through 39 removed outlier: 3.646A pdb=" N GLU G 31 " --> pdb=" O GLU G 27 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 61 removed outlier: 3.796A pdb=" N ILE G 60 " --> pdb=" O TRP G 56 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY G 61 " --> pdb=" O PHE G 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 56 through 61' Processing helix chain 'G' and resid 66 through 77 removed outlier: 4.019A pdb=" N HIS G 71 " --> pdb=" O ARG G 67 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU G 72 " --> pdb=" O LYS G 68 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS G 75 " --> pdb=" O HIS G 71 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN G 76 " --> pdb=" O GLU G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 94 removed outlier: 3.603A pdb=" N ILE G 88 " --> pdb=" O ALA G 84 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA G 91 " --> pdb=" O LYS G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 168 Processing helix chain 'G' and resid 169 through 178 removed outlier: 3.859A pdb=" N LEU G 173 " --> pdb=" O VAL G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 206 Processing helix chain 'G' and resid 217 through 223 Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 273 through 278 removed outlier: 3.720A pdb=" N TYR G 278 " --> pdb=" O ILE G 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 37 removed outlier: 4.270A pdb=" N GLU H 27 " --> pdb=" O GLU H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 61 removed outlier: 3.762A pdb=" N ILE H 60 " --> pdb=" O TRP H 56 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY H 61 " --> pdb=" O PHE H 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 56 through 61' Processing helix chain 'H' and resid 65 through 75 removed outlier: 4.080A pdb=" N PHE H 69 " --> pdb=" O TYR H 65 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HIS H 71 " --> pdb=" O ARG H 67 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLU H 72 " --> pdb=" O LYS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 96 removed outlier: 3.816A pdb=" N ASN H 95 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 140 Processing helix chain 'H' and resid 165 through 168 Processing helix chain 'H' and resid 169 through 178 removed outlier: 3.718A pdb=" N LEU H 173 " --> pdb=" O VAL H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 205 Processing helix chain 'H' and resid 217 through 222 Processing helix chain 'H' and resid 227 through 235 Processing helix chain 'H' and resid 272 through 278 removed outlier: 4.424A pdb=" N TYR H 276 " --> pdb=" O ARG H 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 39 removed outlier: 3.940A pdb=" N GLU I 27 " --> pdb=" O GLU I 23 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS I 30 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU I 31 " --> pdb=" O GLU I 27 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU I 32 " --> pdb=" O LYS I 28 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN I 39 " --> pdb=" O GLU I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 60 removed outlier: 3.734A pdb=" N ILE I 60 " --> pdb=" O PHE I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 75 removed outlier: 4.126A pdb=" N GLU I 72 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS I 75 " --> pdb=" O HIS I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 94 removed outlier: 3.884A pdb=" N ILE I 88 " --> pdb=" O ALA I 84 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA I 91 " --> pdb=" O LYS I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 140 removed outlier: 3.731A pdb=" N LEU I 139 " --> pdb=" O ALA I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 149 removed outlier: 3.733A pdb=" N MET I 149 " --> pdb=" O GLY I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 168 Processing helix chain 'I' and resid 169 through 178 removed outlier: 3.751A pdb=" N LEU I 173 " --> pdb=" O VAL I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 206 removed outlier: 4.149A pdb=" N SER I 197 " --> pdb=" O ASP I 193 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR I 200 " --> pdb=" O ILE I 196 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR I 201 " --> pdb=" O SER I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 219 No H-bonds generated for 'chain 'I' and resid 217 through 219' Processing helix chain 'I' and resid 220 through 225 removed outlier: 3.865A pdb=" N CYS I 225 " --> pdb=" O LYS I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 234 Processing helix chain 'I' and resid 269 through 272 Processing helix chain 'I' and resid 273 through 278 Processing helix chain 'J' and resid 21 through 39 removed outlier: 3.583A pdb=" N SER J 25 " --> pdb=" O ASN J 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU J 27 " --> pdb=" O GLU J 23 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN J 39 " --> pdb=" O GLU J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.601A pdb=" N ILE J 60 " --> pdb=" O TRP J 56 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY J 61 " --> pdb=" O PHE J 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 61' Processing helix chain 'J' and resid 65 through 75 removed outlier: 4.349A pdb=" N PHE J 69 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU J 72 " --> pdb=" O LYS J 68 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS J 75 " --> pdb=" O HIS J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 94 removed outlier: 3.785A pdb=" N GLN J 86 " --> pdb=" O SER J 82 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS J 87 " --> pdb=" O LEU J 83 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE J 88 " --> pdb=" O ALA J 84 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA J 91 " --> pdb=" O LYS J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 168 removed outlier: 3.661A pdb=" N HIS J 167 " --> pdb=" O CYS J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 179 removed outlier: 3.588A pdb=" N LEU J 173 " --> pdb=" O VAL J 169 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN J 179 " --> pdb=" O ALA J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 206 removed outlier: 3.596A pdb=" N ILE J 203 " --> pdb=" O ARG J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 225 removed outlier: 3.894A pdb=" N LYS J 221 " --> pdb=" O THR J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 235 removed outlier: 3.937A pdb=" N TYR J 233 " --> pdb=" O GLU J 229 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU J 235 " --> pdb=" O ARG J 231 " (cutoff:3.500A) Processing helix chain 'J' and resid 273 through 278 removed outlier: 3.579A pdb=" N LYS J 277 " --> pdb=" O VAL J 273 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR J 278 " --> pdb=" O ILE J 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 273 through 278' Processing helix chain 'K' and resid 21 through 39 removed outlier: 4.169A pdb=" N GLU K 27 " --> pdb=" O GLU K 23 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS K 30 " --> pdb=" O VAL K 26 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU K 31 " --> pdb=" O GLU K 27 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN K 39 " --> pdb=" O GLU K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 59 Processing helix chain 'K' and resid 62 through 74 removed outlier: 4.251A pdb=" N LYS K 68 " --> pdb=" O GLU K 64 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE K 69 " --> pdb=" O TYR K 65 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU K 72 " --> pdb=" O LYS K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 77 No H-bonds generated for 'chain 'K' and resid 75 through 77' Processing helix chain 'K' and resid 82 through 95 removed outlier: 3.886A pdb=" N GLN K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE K 88 " --> pdb=" O ALA K 84 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 140 removed outlier: 3.913A pdb=" N ARG K 138 " --> pdb=" O VAL K 135 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU K 139 " --> pdb=" O ALA K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 168 Processing helix chain 'K' and resid 169 through 178 removed outlier: 3.654A pdb=" N LEU K 173 " --> pdb=" O VAL K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 206 removed outlier: 4.016A pdb=" N SER K 197 " --> pdb=" O ASP K 193 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR K 201 " --> pdb=" O SER K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 217 through 225 removed outlier: 3.726A pdb=" N LYS K 221 " --> pdb=" O THR K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 234 Processing helix chain 'K' and resid 269 through 272 Processing helix chain 'K' and resid 273 through 278 removed outlier: 3.761A pdb=" N TYR K 278 " --> pdb=" O ILE K 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 37 removed outlier: 4.121A pdb=" N GLU L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU L 35 " --> pdb=" O GLU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 40 No H-bonds generated for 'chain 'L' and resid 38 through 40' Processing helix chain 'L' and resid 55 through 60 removed outlier: 3.632A pdb=" N ILE L 60 " --> pdb=" O PHE L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 74 removed outlier: 4.247A pdb=" N LYS L 68 " --> pdb=" O GLU L 64 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE L 69 " --> pdb=" O TYR L 65 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU L 72 " --> pdb=" O LYS L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 77 No H-bonds generated for 'chain 'L' and resid 75 through 77' Processing helix chain 'L' and resid 82 through 94 removed outlier: 4.017A pdb=" N ILE L 88 " --> pdb=" O ALA L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 140 removed outlier: 3.712A pdb=" N LEU L 139 " --> pdb=" O ALA L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 168 Processing helix chain 'L' and resid 169 through 178 Processing helix chain 'L' and resid 194 through 206 removed outlier: 3.719A pdb=" N SER L 198 " --> pdb=" O ASP L 194 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE L 203 " --> pdb=" O ARG L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 217 through 225 removed outlier: 3.905A pdb=" N LYS L 221 " --> pdb=" O THR L 217 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET L 223 " --> pdb=" O GLU L 219 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS L 225 " --> pdb=" O LYS L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 234 Processing helix chain 'L' and resid 235 through 237 No H-bonds generated for 'chain 'L' and resid 235 through 237' Processing helix chain 'L' and resid 271 through 277 removed outlier: 4.053A pdb=" N ASP L 275 " --> pdb=" O ARG L 272 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR L 276 " --> pdb=" O VAL L 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 39 removed outlier: 3.517A pdb=" N CYS M 30 " --> pdb=" O VAL M 26 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP M 34 " --> pdb=" O CYS M 30 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN M 39 " --> pdb=" O GLU M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 60 removed outlier: 3.808A pdb=" N ILE M 60 " --> pdb=" O PHE M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 77 removed outlier: 4.276A pdb=" N LYS M 68 " --> pdb=" O GLU M 64 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE M 69 " --> pdb=" O TYR M 65 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS M 71 " --> pdb=" O ARG M 67 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU M 72 " --> pdb=" O LYS M 68 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS M 75 " --> pdb=" O HIS M 71 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN M 76 " --> pdb=" O GLU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 95 removed outlier: 4.375A pdb=" N ALA M 91 " --> pdb=" O LYS M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 140 removed outlier: 3.972A pdb=" N LEU M 139 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 168 Processing helix chain 'M' and resid 169 through 178 removed outlier: 3.866A pdb=" N LEU M 173 " --> pdb=" O VAL M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 206 removed outlier: 3.796A pdb=" N TYR M 201 " --> pdb=" O SER M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 217 through 219 No H-bonds generated for 'chain 'M' and resid 217 through 219' Processing helix chain 'M' and resid 220 through 225 Processing helix chain 'M' and resid 227 through 235 Processing helix chain 'M' and resid 273 through 278 removed outlier: 3.802A pdb=" N TYR M 278 " --> pdb=" O ILE M 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 37 removed outlier: 4.112A pdb=" N GLU N 27 " --> pdb=" O GLU N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 40 No H-bonds generated for 'chain 'N' and resid 38 through 40' Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'N' and resid 66 through 74 removed outlier: 4.470A pdb=" N GLU N 72 " --> pdb=" O LYS N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 95 removed outlier: 4.136A pdb=" N ILE N 88 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA N 91 " --> pdb=" O LYS N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 140 removed outlier: 4.289A pdb=" N LEU N 139 " --> pdb=" O ALA N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 168 Processing helix chain 'N' and resid 169 through 178 removed outlier: 3.827A pdb=" N LEU N 173 " --> pdb=" O VAL N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 206 removed outlier: 3.767A pdb=" N TYR N 201 " --> pdb=" O SER N 197 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA N 202 " --> pdb=" O SER N 198 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE N 203 " --> pdb=" O ARG N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 218 through 223 removed outlier: 4.029A pdb=" N MET N 223 " --> pdb=" O GLU N 219 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.917A pdb=" N TYR N 233 " --> pdb=" O GLU N 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 273 through 278 Processing helix chain 'O' and resid 21 through 39 removed outlier: 3.643A pdb=" N GLU O 27 " --> pdb=" O GLU O 23 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU O 31 " --> pdb=" O GLU O 27 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN O 39 " --> pdb=" O GLU O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 removed outlier: 3.501A pdb=" N PHE O 59 " --> pdb=" O TRP O 56 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE O 60 " --> pdb=" O PHE O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 74 removed outlier: 3.642A pdb=" N THR O 66 " --> pdb=" O HIS O 62 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG O 67 " --> pdb=" O PRO O 63 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS O 68 " --> pdb=" O GLU O 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE O 69 " --> pdb=" O TYR O 65 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU O 72 " --> pdb=" O LYS O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 through 77' Processing helix chain 'O' and resid 82 through 94 removed outlier: 3.736A pdb=" N GLN O 86 " --> pdb=" O SER O 82 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA O 91 " --> pdb=" O LYS O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 140 removed outlier: 3.816A pdb=" N LEU O 139 " --> pdb=" O ALA O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 163 through 168 removed outlier: 3.556A pdb=" N HIS O 167 " --> pdb=" O CYS O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 178 removed outlier: 3.640A pdb=" N LEU O 173 " --> pdb=" O VAL O 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 206 removed outlier: 4.558A pdb=" N TYR O 201 " --> pdb=" O SER O 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 217 through 225 removed outlier: 4.023A pdb=" N LYS O 221 " --> pdb=" O THR O 217 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET O 223 " --> pdb=" O GLU O 219 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS O 225 " --> pdb=" O LYS O 221 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 234 Processing helix chain 'O' and resid 273 through 278 removed outlier: 3.663A pdb=" N LYS O 277 " --> pdb=" O VAL O 273 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR O 278 " --> pdb=" O ILE O 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 273 through 278' Processing helix chain 'P' and resid 21 through 37 removed outlier: 3.518A pdb=" N SER P 25 " --> pdb=" O ASN P 21 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU P 27 " --> pdb=" O GLU P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 40 No H-bonds generated for 'chain 'P' and resid 38 through 40' Processing helix chain 'P' and resid 55 through 59 Processing helix chain 'P' and resid 62 through 74 removed outlier: 3.670A pdb=" N ARG P 67 " --> pdb=" O PRO P 63 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS P 68 " --> pdb=" O GLU P 64 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE P 69 " --> pdb=" O TYR P 65 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS P 71 " --> pdb=" O ARG P 67 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU P 72 " --> pdb=" O LYS P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 77 No H-bonds generated for 'chain 'P' and resid 75 through 77' Processing helix chain 'P' and resid 82 through 95 removed outlier: 4.167A pdb=" N ILE P 88 " --> pdb=" O ALA P 84 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA P 91 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN P 95 " --> pdb=" O ALA P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 140 removed outlier: 3.799A pdb=" N LEU P 139 " --> pdb=" O ALA P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 168 Processing helix chain 'P' and resid 169 through 178 removed outlier: 3.972A pdb=" N LEU P 173 " --> pdb=" O VAL P 169 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET P 174 " --> pdb=" O PRO P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 206 Processing helix chain 'P' and resid 218 through 225 Processing helix chain 'P' and resid 227 through 235 removed outlier: 3.912A pdb=" N ARG P 231 " --> pdb=" O THR P 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 273 through 278 removed outlier: 3.581A pdb=" N TYR P 278 " --> pdb=" O ILE P 274 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 39 removed outlier: 4.456A pdb=" N GLU Q 27 " --> pdb=" O GLU Q 23 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS Q 28 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER Q 29 " --> pdb=" O SER Q 25 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS Q 30 " --> pdb=" O VAL Q 26 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN Q 39 " --> pdb=" O GLU Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 60 removed outlier: 3.627A pdb=" N ILE Q 60 " --> pdb=" O PHE Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 76 removed outlier: 3.830A pdb=" N LYS Q 68 " --> pdb=" O GLU Q 64 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE Q 69 " --> pdb=" O TYR Q 65 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS Q 71 " --> pdb=" O ARG Q 67 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU Q 72 " --> pdb=" O LYS Q 68 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS Q 75 " --> pdb=" O HIS Q 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN Q 76 " --> pdb=" O GLU Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 94 removed outlier: 3.866A pdb=" N GLN Q 86 " --> pdb=" O SER Q 82 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA Q 91 " --> pdb=" O LYS Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 140 removed outlier: 4.038A pdb=" N LEU Q 139 " --> pdb=" O ALA Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 168 Processing helix chain 'Q' and resid 169 through 178 removed outlier: 3.811A pdb=" N LEU Q 173 " --> pdb=" O VAL Q 169 " (cutoff:3.500A) Processing helix chain 'Q' and resid 196 through 206 removed outlier: 3.534A pdb=" N TYR Q 201 " --> pdb=" O SER Q 197 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA Q 202 " --> pdb=" O SER Q 198 " (cutoff:3.500A) Processing helix chain 'Q' and resid 220 through 225 removed outlier: 4.259A pdb=" N CYS Q 225 " --> pdb=" O LYS Q 221 " (cutoff:3.500A) Processing helix chain 'Q' and resid 227 through 234 Processing helix chain 'Q' and resid 235 through 237 No H-bonds generated for 'chain 'Q' and resid 235 through 237' Processing helix chain 'Q' and resid 271 through 276 removed outlier: 4.012A pdb=" N ILE Q 274 " --> pdb=" O GLU Q 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 39 removed outlier: 3.935A pdb=" N GLU R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 59 Processing helix chain 'R' and resid 62 through 74 removed outlier: 3.940A pdb=" N THR R 66 " --> pdb=" O HIS R 62 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG R 67 " --> pdb=" O PRO R 63 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS R 68 " --> pdb=" O GLU R 64 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE R 69 " --> pdb=" O TYR R 65 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU R 72 " --> pdb=" O LYS R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 77 No H-bonds generated for 'chain 'R' and resid 75 through 77' Processing helix chain 'R' and resid 82 through 95 removed outlier: 3.822A pdb=" N GLN R 86 " --> pdb=" O SER R 82 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE R 88 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 140 Processing helix chain 'R' and resid 163 through 168 removed outlier: 3.568A pdb=" N HIS R 167 " --> pdb=" O CYS R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 178 removed outlier: 3.583A pdb=" N LEU R 173 " --> pdb=" O VAL R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 206 removed outlier: 4.701A pdb=" N SER R 197 " --> pdb=" O ASP R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 225 removed outlier: 3.639A pdb=" N LYS R 221 " --> pdb=" O THR R 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET R 223 " --> pdb=" O GLU R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 234 Processing helix chain 'R' and resid 269 through 271 No H-bonds generated for 'chain 'R' and resid 269 through 271' Processing helix chain 'R' and resid 272 through 278 removed outlier: 4.218A pdb=" N TYR R 276 " --> pdb=" O ARG R 272 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 39 removed outlier: 3.919A pdb=" N GLU S 27 " --> pdb=" O GLU S 23 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS S 28 " --> pdb=" O ALA S 24 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN S 39 " --> pdb=" O GLU S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 60 removed outlier: 3.591A pdb=" N PHE S 59 " --> pdb=" O TRP S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 76 removed outlier: 3.898A pdb=" N THR S 66 " --> pdb=" O HIS S 62 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG S 67 " --> pdb=" O PRO S 63 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LYS S 68 " --> pdb=" O GLU S 64 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE S 69 " --> pdb=" O TYR S 65 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU S 72 " --> pdb=" O LYS S 68 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS S 75 " --> pdb=" O HIS S 71 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN S 76 " --> pdb=" O GLU S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 94 removed outlier: 3.907A pdb=" N GLN S 86 " --> pdb=" O SER S 82 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA S 91 " --> pdb=" O LYS S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 140 removed outlier: 3.994A pdb=" N LEU S 139 " --> pdb=" O ALA S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 163 through 168 removed outlier: 3.598A pdb=" N HIS S 167 " --> pdb=" O CYS S 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 169 through 178 removed outlier: 4.120A pdb=" N LEU S 173 " --> pdb=" O VAL S 169 " (cutoff:3.500A) Processing helix chain 'S' and resid 194 through 206 removed outlier: 3.830A pdb=" N TYR S 201 " --> pdb=" O SER S 197 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE S 203 " --> pdb=" O ARG S 199 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 225 removed outlier: 3.897A pdb=" N CYS S 225 " --> pdb=" O LYS S 221 " (cutoff:3.500A) Processing helix chain 'S' and resid 227 through 235 removed outlier: 3.957A pdb=" N GLU S 235 " --> pdb=" O ARG S 231 " (cutoff:3.500A) Processing helix chain 'S' and resid 273 through 278 removed outlier: 3.951A pdb=" N TYR S 278 " --> pdb=" O ILE S 274 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 39 removed outlier: 3.791A pdb=" N GLU U 27 " --> pdb=" O GLU U 23 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN U 39 " --> pdb=" O GLU U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 60 removed outlier: 3.732A pdb=" N PHE U 59 " --> pdb=" O TRP U 56 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE U 60 " --> pdb=" O PHE U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 76 removed outlier: 4.303A pdb=" N ARG U 67 " --> pdb=" O PRO U 63 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LYS U 68 " --> pdb=" O GLU U 64 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE U 69 " --> pdb=" O TYR U 65 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU U 72 " --> pdb=" O LYS U 68 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS U 75 " --> pdb=" O HIS U 71 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN U 76 " --> pdb=" O GLU U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 96 removed outlier: 3.858A pdb=" N GLN U 86 " --> pdb=" O SER U 82 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA U 91 " --> pdb=" O LYS U 87 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN U 95 " --> pdb=" O ALA U 91 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 140 Processing helix chain 'U' and resid 165 through 168 Processing helix chain 'U' and resid 169 through 178 removed outlier: 3.950A pdb=" N LEU U 173 " --> pdb=" O VAL U 169 " (cutoff:3.500A) Processing helix chain 'U' and resid 193 through 206 removed outlier: 4.466A pdb=" N SER U 197 " --> pdb=" O ASP U 193 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER U 198 " --> pdb=" O ASP U 194 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR U 201 " --> pdb=" O SER U 197 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE U 203 " --> pdb=" O ARG U 199 " (cutoff:3.500A) Processing helix chain 'U' and resid 217 through 219 No H-bonds generated for 'chain 'U' and resid 217 through 219' Processing helix chain 'U' and resid 220 through 225 Processing helix chain 'U' and resid 227 through 235 removed outlier: 3.904A pdb=" N TYR U 233 " --> pdb=" O GLU U 229 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU U 235 " --> pdb=" O ARG U 231 " (cutoff:3.500A) Processing helix chain 'U' and resid 271 through 274 removed outlier: 3.644A pdb=" N ILE U 274 " --> pdb=" O GLU U 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 271 through 274' Processing sheet with id=AA1, first strand: chain 'B' and resid 123 through 129 removed outlier: 7.296A pdb=" N TRP B 117 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS B 127 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN B 115 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ARG B 129 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU B 113 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 44 " --> pdb=" O CYS B 100 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N SER B 102 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B 43 " --> pdb=" O ARG B 9 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 45 " --> pdb=" O ALA B 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 159 through 163 removed outlier: 7.015A pdb=" N GLY B 160 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N SER B 187 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU B 162 " --> pdb=" O SER B 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 303 through 306 removed outlier: 3.661A pdb=" N PHE D 295 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 124 through 129 removed outlier: 4.192A pdb=" N GLY D 126 " --> pdb=" O TRP D 117 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP D 117 " --> pdb=" O GLY D 126 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER D 110 " --> pdb=" O ASP D 107 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP D 107 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL D 44 " --> pdb=" O CYS D 100 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N SER D 102 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU D 43 " --> pdb=" O ARG D 9 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 266 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.693A pdb=" N GLY D 160 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL D 185 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 187 " --> pdb=" O LEU D 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 303 through 308 removed outlier: 3.526A pdb=" N PHE F 295 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLN F 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N HIS D 308 " --> pdb=" O GLN F 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 124 through 129 removed outlier: 7.289A pdb=" N TRP F 117 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS F 127 " --> pdb=" O GLN F 115 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN F 115 " --> pdb=" O LYS F 127 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ARG F 129 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU F 113 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL F 44 " --> pdb=" O CYS F 100 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N SER F 102 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU F 43 " --> pdb=" O ARG F 9 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA F 266 " --> pdb=" O ALA F 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 159 through 163 Processing sheet with id=AA9, first strand: chain 'F' and resid 303 through 306 removed outlier: 6.337A pdb=" N LYS F 304 " --> pdb=" O PHE H 295 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS I 304 " --> pdb=" O MET G 293 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE G 295 " --> pdb=" O LYS I 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 124 through 129 removed outlier: 7.017A pdb=" N TRP G 117 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS G 127 " --> pdb=" O GLN G 115 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLN G 115 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ARG G 129 " --> pdb=" O LEU G 113 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU G 113 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G 99 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU G 43 " --> pdb=" O ARG G 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 152 through 154 removed outlier: 3.677A pdb=" N THR G 154 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN G 158 " --> pdb=" O VAL G 183 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL G 185 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY G 160 " --> pdb=" O VAL G 185 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N SER G 187 " --> pdb=" O GLY G 160 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU G 162 " --> pdb=" O SER G 187 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 124 through 129 removed outlier: 7.240A pdb=" N TRP H 117 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS H 127 " --> pdb=" O GLN H 115 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN H 115 " --> pdb=" O LYS H 127 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG H 129 " --> pdb=" O LEU H 113 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU H 113 " --> pdb=" O ARG H 129 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL H 44 " --> pdb=" O CYS H 100 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N SER H 102 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU H 43 " --> pdb=" O ARG H 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 152 through 154 removed outlier: 3.637A pdb=" N GLY H 160 " --> pdb=" O VAL H 183 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA H 186 " --> pdb=" O LEU H 210 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 304 through 306 removed outlier: 3.506A pdb=" N PHE J 295 " --> pdb=" O LYS H 304 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 124 through 129 removed outlier: 7.082A pdb=" N TRP I 117 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS I 127 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN I 115 " --> pdb=" O LYS I 127 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ARG I 129 " --> pdb=" O LEU I 113 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU I 113 " --> pdb=" O ARG I 129 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL I 44 " --> pdb=" O CYS I 100 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N SER I 102 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU I 43 " --> pdb=" O ARG I 9 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA I 266 " --> pdb=" O ALA I 10 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 152 through 154 removed outlier: 6.437A pdb=" N ASN I 158 " --> pdb=" O VAL I 183 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL I 185 " --> pdb=" O ASN I 158 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY I 160 " --> pdb=" O VAL I 185 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N SER I 187 " --> pdb=" O GLY I 160 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU I 162 " --> pdb=" O SER I 187 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N HIS I 184 " --> pdb=" O LEU I 210 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR I 212 " --> pdb=" O HIS I 184 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA I 186 " --> pdb=" O THR I 212 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 293 through 296 removed outlier: 7.188A pdb=" N MET I 293 " --> pdb=" O LYS K 304 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU K 306 " --> pdb=" O MET I 293 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N PHE I 295 " --> pdb=" O LEU K 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'J' and resid 124 through 129 removed outlier: 4.155A pdb=" N GLY J 126 " --> pdb=" O TRP J 117 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL J 44 " --> pdb=" O CYS J 100 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N SER J 102 " --> pdb=" O VAL J 44 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU J 43 " --> pdb=" O ARG J 9 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA J 45 " --> pdb=" O ALA J 11 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.907A pdb=" N GLY J 160 " --> pdb=" O VAL J 185 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N SER J 187 " --> pdb=" O GLY J 160 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU J 210 " --> pdb=" O HIS J 184 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA J 186 " --> pdb=" O LEU J 210 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 304 through 306 removed outlier: 3.579A pdb=" N SER L 292 " --> pdb=" O ASN K 294 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN K 294 " --> pdb=" O SER L 292 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS M 304 " --> pdb=" O MET K 293 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 124 through 129 removed outlier: 7.286A pdb=" N TRP K 117 " --> pdb=" O ILE K 125 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLN K 115 " --> pdb=" O LYS K 127 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ARG K 129 " --> pdb=" O LEU K 113 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU K 113 " --> pdb=" O ARG K 129 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU K 43 " --> pdb=" O ARG K 9 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA K 45 " --> pdb=" O ALA K 11 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL K 13 " --> pdb=" O ALA K 45 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 159 through 163 removed outlier: 7.012A pdb=" N GLY K 160 " --> pdb=" O VAL K 185 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N SER K 187 " --> pdb=" O GLY K 160 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU K 162 " --> pdb=" O SER K 187 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N HIS K 184 " --> pdb=" O LEU K 210 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N THR K 212 " --> pdb=" O HIS K 184 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA K 186 " --> pdb=" O THR K 212 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 124 through 129 removed outlier: 7.156A pdb=" N TRP L 117 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS L 127 " --> pdb=" O GLN L 115 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN L 115 " --> pdb=" O LYS L 127 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ARG L 129 " --> pdb=" O LEU L 113 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU L 113 " --> pdb=" O ARG L 129 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL L 44 " --> pdb=" O CYS L 100 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N SER L 102 " --> pdb=" O VAL L 44 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU L 43 " --> pdb=" O ARG L 9 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA L 45 " --> pdb=" O ALA L 11 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 159 through 163 removed outlier: 6.930A pdb=" N GLY L 160 " --> pdb=" O VAL L 185 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N SER L 187 " --> pdb=" O GLY L 160 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU L 162 " --> pdb=" O SER L 187 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N HIS L 184 " --> pdb=" O LEU L 210 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N THR L 212 " --> pdb=" O HIS L 184 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA L 186 " --> pdb=" O THR L 212 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 303 through 306 removed outlier: 3.501A pdb=" N PHE N 295 " --> pdb=" O LYS L 304 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER M 292 " --> pdb=" O ASN N 294 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N LYS O 304 " --> pdb=" O LEU M 291 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N MET M 293 " --> pdb=" O LYS O 304 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 124 through 129 removed outlier: 3.838A pdb=" N GLY M 126 " --> pdb=" O TRP M 117 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL M 44 " --> pdb=" O CYS M 100 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N SER M 102 " --> pdb=" O VAL M 44 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU M 43 " --> pdb=" O ARG M 9 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 106 through 107 Processing sheet with id=AD1, first strand: chain 'M' and resid 152 through 153 removed outlier: 3.595A pdb=" N GLY M 160 " --> pdb=" O VAL M 183 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER M 187 " --> pdb=" O LEU M 162 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N HIS M 184 " --> pdb=" O LEU M 210 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR M 212 " --> pdb=" O HIS M 184 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA M 186 " --> pdb=" O THR M 212 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 124 through 129 removed outlier: 7.281A pdb=" N TRP N 117 " --> pdb=" O ILE N 125 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS N 127 " --> pdb=" O GLN N 115 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN N 115 " --> pdb=" O LYS N 127 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG N 129 " --> pdb=" O LEU N 113 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU N 113 " --> pdb=" O ARG N 129 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL N 44 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N SER N 102 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU N 43 " --> pdb=" O ARG N 9 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 152 through 154 removed outlier: 6.418A pdb=" N ASN N 158 " --> pdb=" O VAL N 183 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL N 185 " --> pdb=" O ASN N 158 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY N 160 " --> pdb=" O VAL N 185 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N SER N 187 " --> pdb=" O GLY N 160 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU N 162 " --> pdb=" O SER N 187 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA N 186 " --> pdb=" O LEU N 210 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 303 through 306 removed outlier: 3.538A pdb=" N PHE P 295 " --> pdb=" O LYS N 304 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER O 292 " --> pdb=" O ASN P 294 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS Q 304 " --> pdb=" O MET O 293 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE O 295 " --> pdb=" O LYS Q 304 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 124 through 129 removed outlier: 7.184A pdb=" N TRP O 117 " --> pdb=" O ILE O 125 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LYS O 127 " --> pdb=" O GLN O 115 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN O 115 " --> pdb=" O LYS O 127 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG O 129 " --> pdb=" O LEU O 113 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU O 113 " --> pdb=" O ARG O 129 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL O 44 " --> pdb=" O CYS O 100 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N SER O 102 " --> pdb=" O VAL O 44 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU O 43 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA O 45 " --> pdb=" O ALA O 11 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 159 through 160 removed outlier: 6.928A pdb=" N GLY O 160 " --> pdb=" O VAL O 185 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N SER O 187 " --> pdb=" O GLY O 160 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 124 through 129 removed outlier: 3.977A pdb=" N GLY P 126 " --> pdb=" O TRP P 117 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL P 44 " --> pdb=" O CYS P 100 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N SER P 102 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU P 43 " --> pdb=" O ARG P 9 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 152 through 154 removed outlier: 6.412A pdb=" N ASN P 158 " --> pdb=" O VAL P 183 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL P 185 " --> pdb=" O ASN P 158 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY P 160 " --> pdb=" O VAL P 185 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N SER P 187 " --> pdb=" O GLY P 160 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU P 162 " --> pdb=" O SER P 187 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N HIS P 184 " --> pdb=" O LEU P 210 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N THR P 212 " --> pdb=" O HIS P 184 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA P 186 " --> pdb=" O THR P 212 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 303 through 306 removed outlier: 6.005A pdb=" N LYS P 304 " --> pdb=" O PHE R 295 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N LYS S 304 " --> pdb=" O LEU Q 291 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N MET Q 293 " --> pdb=" O LYS S 304 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LEU S 306 " --> pdb=" O MET Q 293 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE Q 295 " --> pdb=" O LEU S 306 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 124 through 129 removed outlier: 7.051A pdb=" N TRP Q 117 " --> pdb=" O ILE Q 125 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS Q 127 " --> pdb=" O GLN Q 115 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLN Q 115 " --> pdb=" O LYS Q 127 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL Q 44 " --> pdb=" O CYS Q 100 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N SER Q 102 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU Q 43 " --> pdb=" O ARG Q 9 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 162 through 163 removed outlier: 6.971A pdb=" N LEU Q 162 " --> pdb=" O SER Q 187 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N HIS Q 184 " --> pdb=" O LEU Q 210 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N THR Q 212 " --> pdb=" O HIS Q 184 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA Q 186 " --> pdb=" O THR Q 212 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 124 through 129 removed outlier: 7.284A pdb=" N TRP R 117 " --> pdb=" O ILE R 125 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS R 127 " --> pdb=" O GLN R 115 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLN R 115 " --> pdb=" O LYS R 127 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG R 129 " --> pdb=" O LEU R 113 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU R 113 " --> pdb=" O ARG R 129 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL R 99 " --> pdb=" O PHE R 118 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU R 43 " --> pdb=" O ARG R 9 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA R 45 " --> pdb=" O ALA R 11 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL R 13 " --> pdb=" O ALA R 45 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 159 through 160 removed outlier: 7.039A pdb=" N GLY R 160 " --> pdb=" O VAL R 185 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N SER R 187 " --> pdb=" O GLY R 160 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N HIS R 184 " --> pdb=" O LEU R 210 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR R 212 " --> pdb=" O HIS R 184 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA R 186 " --> pdb=" O THR R 212 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 124 through 129 removed outlier: 6.998A pdb=" N TRP S 117 " --> pdb=" O ILE S 125 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS S 127 " --> pdb=" O GLN S 115 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN S 115 " --> pdb=" O LYS S 127 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL S 44 " --> pdb=" O CYS S 100 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N SER S 102 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU S 43 " --> pdb=" O ARG S 9 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL S 13 " --> pdb=" O ALA S 45 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 106 through 107 Processing sheet with id=AE7, first strand: chain 'S' and resid 159 through 160 removed outlier: 6.776A pdb=" N GLY S 160 " --> pdb=" O VAL S 185 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N SER S 187 " --> pdb=" O GLY S 160 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 293 through 295 removed outlier: 7.162A pdb=" N MET S 293 " --> pdb=" O LYS U 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'U' and resid 98 through 100 removed outlier: 3.924A pdb=" N LEU U 43 " --> pdb=" O ARG U 9 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL U 13 " --> pdb=" O ALA U 45 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'U' and resid 102 through 107 removed outlier: 7.459A pdb=" N LEU U 113 " --> pdb=" O ARG U 129 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG U 129 " --> pdb=" O LEU U 113 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN U 115 " --> pdb=" O LYS U 127 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS U 127 " --> pdb=" O GLN U 115 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TRP U 117 " --> pdb=" O ILE U 125 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP U 123 " --> pdb=" O ASN U 119 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'U' and resid 152 through 154 removed outlier: 3.551A pdb=" N PHE U 152 " --> pdb=" O LEU U 159 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU U 159 " --> pdb=" O PHE U 152 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASN U 158 " --> pdb=" O VAL U 183 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL U 185 " --> pdb=" O ASN U 158 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY U 160 " --> pdb=" O VAL U 185 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N SER U 187 " --> pdb=" O GLY U 160 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU U 162 " --> pdb=" O SER U 187 " (cutoff:3.500A) 1321 hydrogen bonds defined for protein. 3537 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.49 Time building geometry restraints manager: 16.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11740 1.33 - 1.46: 8470 1.46 - 1.58: 23462 1.58 - 1.70: 1 1.70 - 1.82: 476 Bond restraints: 44149 Sorted by residual: bond pdb=" ND1 HIS P 305 " pdb=" CE1 HIS P 305 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.82e+01 bond pdb=" CG ASN L 294 " pdb=" OD1 ASN L 294 " ideal model delta sigma weight residual 1.231 1.327 -0.096 1.90e-02 2.77e+03 2.53e+01 bond pdb=" CG ASN R 294 " pdb=" OD1 ASN R 294 " ideal model delta sigma weight residual 1.231 1.326 -0.095 1.90e-02 2.77e+03 2.51e+01 bond pdb=" CD GLN S 297 " pdb=" OE1 GLN S 297 " ideal model delta sigma weight residual 1.231 1.326 -0.095 1.90e-02 2.77e+03 2.51e+01 bond pdb=" CG ASN K 294 " pdb=" OD1 ASN K 294 " ideal model delta sigma weight residual 1.231 1.326 -0.095 1.90e-02 2.77e+03 2.50e+01 ... (remaining 44144 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.66: 1280 105.66 - 113.17: 20433 113.17 - 120.67: 23473 120.67 - 128.18: 14480 128.18 - 135.69: 293 Bond angle restraints: 59959 Sorted by residual: angle pdb=" N MET H 131 " pdb=" CA MET H 131 " pdb=" C MET H 131 " ideal model delta sigma weight residual 110.97 119.17 -8.20 1.09e+00 8.42e-01 5.66e+01 angle pdb=" N VAL M 135 " pdb=" CA VAL M 135 " pdb=" C VAL M 135 " ideal model delta sigma weight residual 110.36 117.30 -6.94 1.05e+00 9.07e-01 4.37e+01 angle pdb=" CB HIS P 305 " pdb=" CG HIS P 305 " pdb=" CD2 HIS P 305 " ideal model delta sigma weight residual 131.20 122.63 8.57 1.30e+00 5.92e-01 4.35e+01 angle pdb=" N VAL Q 99 " pdb=" CA VAL Q 99 " pdb=" C VAL Q 99 " ideal model delta sigma weight residual 107.78 117.18 -9.40 1.49e+00 4.50e-01 3.98e+01 angle pdb=" N TYR F 233 " pdb=" CA TYR F 233 " pdb=" C TYR F 233 " ideal model delta sigma weight residual 111.36 104.53 6.83 1.09e+00 8.42e-01 3.93e+01 ... (remaining 59954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 23855 17.91 - 35.83: 1767 35.83 - 53.74: 435 53.74 - 71.65: 108 71.65 - 89.56: 49 Dihedral angle restraints: 26214 sinusoidal: 10370 harmonic: 15844 Sorted by residual: dihedral pdb=" CA VAL G 256 " pdb=" C VAL G 256 " pdb=" N PRO G 257 " pdb=" CA PRO G 257 " ideal model delta harmonic sigma weight residual 180.00 -150.30 -29.70 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ILE L 18 " pdb=" C ILE L 18 " pdb=" N TYR L 19 " pdb=" CA TYR L 19 " ideal model delta harmonic sigma weight residual -180.00 -150.89 -29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA TYR I 5 " pdb=" C TYR I 5 " pdb=" N PRO I 6 " pdb=" CA PRO I 6 " ideal model delta harmonic sigma weight residual -180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 26211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 4500 0.092 - 0.183: 1492 0.183 - 0.275: 236 0.275 - 0.367: 51 0.367 - 0.459: 11 Chirality restraints: 6290 Sorted by residual: chirality pdb=" CA GLU D 96 " pdb=" N GLU D 96 " pdb=" C GLU D 96 " pdb=" CB GLU D 96 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" CA PHE M 192 " pdb=" N PHE M 192 " pdb=" C PHE M 192 " pdb=" CB PHE M 192 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.05e+00 chirality pdb=" CA GLU J 96 " pdb=" N GLU J 96 " pdb=" C GLU J 96 " pdb=" CB GLU J 96 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 6287 not shown) Planarity restraints: 7837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 165 " 0.144 2.00e-02 2.50e+03 6.77e-02 1.15e+02 pdb=" CG TRP D 165 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP D 165 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP D 165 " -0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP D 165 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP D 165 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 165 " -0.085 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 165 " 0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 165 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP D 165 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 165 " 0.129 2.00e-02 2.50e+03 6.00e-02 9.01e+01 pdb=" CG TRP P 165 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP P 165 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP P 165 " -0.061 2.00e-02 2.50e+03 pdb=" NE1 TRP P 165 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP P 165 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP P 165 " -0.067 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 165 " 0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 165 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP P 165 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 165 " 0.121 2.00e-02 2.50e+03 5.63e-02 7.94e+01 pdb=" CG TRP H 165 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP H 165 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP H 165 " -0.053 2.00e-02 2.50e+03 pdb=" NE1 TRP H 165 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP H 165 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP H 165 " -0.062 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 165 " 0.053 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 165 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP H 165 " 0.054 2.00e-02 2.50e+03 ... (remaining 7834 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5102 2.79 - 3.32: 41613 3.32 - 3.85: 61498 3.85 - 4.37: 75035 4.37 - 4.90: 129603 Nonbonded interactions: 312851 Sorted by model distance: nonbonded pdb=" O THR P 300 " pdb=" OG1 THR P 300 " model vdw 2.265 2.440 nonbonded pdb=" O THR B 300 " pdb=" OG1 THR B 300 " model vdw 2.276 2.440 nonbonded pdb=" O THR N 300 " pdb=" OG1 THR N 300 " model vdw 2.294 2.440 nonbonded pdb=" O THR O 300 " pdb=" OG1 THR O 300 " model vdw 2.325 2.440 nonbonded pdb=" OD1 ASP R 318 " pdb=" N ILE R 319 " model vdw 2.352 2.520 ... (remaining 312846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 8.060 Check model and map are aligned: 0.570 Set scattering table: 0.350 Process input model: 102.770 Find NCS groups from input model: 2.780 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.098 44149 Z= 0.791 Angle : 1.734 12.815 59959 Z= 1.157 Chirality : 0.092 0.459 6290 Planarity : 0.012 0.129 7837 Dihedral : 14.633 89.564 16082 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.84 % Favored : 94.92 % Rotamer: Outliers : 1.50 % Allowed : 6.84 % Favored : 91.66 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.10), residues: 5355 helix: -2.61 (0.10), residues: 1581 sheet: 0.30 (0.16), residues: 850 loop : -1.35 (0.11), residues: 2924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.144 0.018 TRP D 165 HIS 0.015 0.002 HIS J 71 PHE 0.080 0.009 PHE J 59 TYR 0.108 0.017 TYR U 65 ARG 0.008 0.001 ARG O 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 616 time to evaluate : 4.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 MET cc_start: 0.7598 (tpt) cc_final: 0.6876 (tpt) REVERT: B 132 ARG cc_start: 0.7218 (mmt90) cc_final: 0.6806 (ttp-170) REVERT: B 211 MET cc_start: 0.7787 (ttp) cc_final: 0.7542 (ttp) REVERT: B 255 MET cc_start: 0.6822 (tpp) cc_final: 0.6600 (tpp) REVERT: B 268 ILE cc_start: 0.9261 (mt) cc_final: 0.8878 (mm) REVERT: F 94 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7568 (ttm110) REVERT: F 132 ARG cc_start: 0.7453 (ttt-90) cc_final: 0.6763 (ptt180) REVERT: F 220 MET cc_start: 0.8954 (ptp) cc_final: 0.8726 (ptp) REVERT: G 131 MET cc_start: 0.8234 (mmt) cc_final: 0.7960 (mmm) REVERT: G 180 ASN cc_start: 0.8702 (t0) cc_final: 0.8426 (t0) REVERT: H 281 ASP cc_start: 0.8205 (t0) cc_final: 0.7626 (t0) REVERT: I 255 MET cc_start: 0.7764 (tpp) cc_final: 0.7409 (tpp) REVERT: J 255 MET cc_start: 0.7876 (tpp) cc_final: 0.7483 (tpp) REVERT: K 123 ASP cc_start: 0.8357 (p0) cc_final: 0.8127 (p0) REVERT: K 125 ILE cc_start: 0.9297 (mt) cc_final: 0.8927 (mm) REVERT: K 152 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.7525 (p90) REVERT: K 255 MET cc_start: 0.8100 (tpp) cc_final: 0.7162 (tpt) REVERT: L 94 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7630 (ttp80) REVERT: L 123 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.7993 (p0) REVERT: L 201 TYR cc_start: 0.8875 (t80) cc_final: 0.8625 (t80) REVERT: M 143 ASP cc_start: 0.6961 (t0) cc_final: 0.6662 (m-30) REVERT: M 163 MET cc_start: 0.8236 (mtp) cc_final: 0.7479 (mtp) REVERT: M 255 MET cc_start: 0.7448 (tpp) cc_final: 0.7064 (tpp) REVERT: N 117 TRP cc_start: 0.9095 (m100) cc_final: 0.8479 (m100) REVERT: N 281 ASP cc_start: 0.8457 (t0) cc_final: 0.8252 (t70) REVERT: O 125 ILE cc_start: 0.9379 (mt) cc_final: 0.9118 (mm) REVERT: O 138 ARG cc_start: 0.8756 (ptp-170) cc_final: 0.8551 (ptp-170) REVERT: O 163 MET cc_start: 0.7889 (mtp) cc_final: 0.6961 (mtp) REVERT: O 180 ASN cc_start: 0.8725 (t0) cc_final: 0.8443 (t0) REVERT: O 220 MET cc_start: 0.7658 (ptm) cc_final: 0.7445 (ptm) REVERT: Q 255 MET cc_start: 0.7151 (tpp) cc_final: 0.6450 (tpp) REVERT: Q 305 HIS cc_start: 0.8580 (m90) cc_final: 0.8365 (m90) REVERT: R 86 GLN cc_start: 0.7310 (tt0) cc_final: 0.6870 (tt0) REVERT: R 125 ILE cc_start: 0.9204 (mt) cc_final: 0.8899 (mm) REVERT: R 129 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7594 (mtt-85) REVERT: R 148 MET cc_start: 0.8891 (mtt) cc_final: 0.8554 (mtm) REVERT: R 174 MET cc_start: 0.9386 (tpp) cc_final: 0.9090 (tpp) REVERT: S 149 MET cc_start: 0.8776 (ttm) cc_final: 0.8564 (ttt) REVERT: S 220 MET cc_start: 0.7765 (ttm) cc_final: 0.7468 (ttm) REVERT: U 82 SER cc_start: 0.8609 (t) cc_final: 0.8280 (p) REVERT: U 132 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.6318 (ttp-170) REVERT: U 149 MET cc_start: 0.8811 (ttp) cc_final: 0.8584 (ttt) REVERT: U 176 MET cc_start: 0.9306 (tpp) cc_final: 0.8590 (tpp) REVERT: U 199 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8107 (ttm-80) REVERT: U 234 PHE cc_start: 0.8829 (t80) cc_final: 0.8593 (t80) REVERT: U 255 MET cc_start: 0.7720 (tpp) cc_final: 0.7457 (tpp) REVERT: U 281 ASP cc_start: 0.8318 (t0) cc_final: 0.7857 (t70) outliers start: 69 outliers final: 21 residues processed: 675 average time/residue: 0.5913 time to fit residues: 646.8097 Evaluate side-chains 412 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 387 time to evaluate : 5.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain L residue 123 ASP Chi-restraints excluded: chain M residue 134 SER Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 298 GLN Chi-restraints excluded: chain O residue 303 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain Q residue 303 VAL Chi-restraints excluded: chain R residue 65 TYR Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 315 THR Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 265 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 445 optimal weight: 0.8980 chunk 399 optimal weight: 0.9990 chunk 221 optimal weight: 0.6980 chunk 136 optimal weight: 7.9990 chunk 269 optimal weight: 8.9990 chunk 213 optimal weight: 4.9990 chunk 413 optimal weight: 0.9990 chunk 159 optimal weight: 0.2980 chunk 251 optimal weight: 1.9990 chunk 307 optimal weight: 2.9990 chunk 478 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN B 228 GLN D 115 GLN D 119 ASN ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN G 294 ASN G 297 GLN ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 HIS H 294 ASN ** J 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 294 ASN L 294 ASN N 308 HIS O 119 ASN O 228 GLN O 309 GLN ** P 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 158 ASN Q 167 HIS Q 177 ASN Q 180 ASN U 228 GLN U 285 HIS U 307 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 44149 Z= 0.169 Angle : 0.637 15.741 59959 Z= 0.335 Chirality : 0.044 0.213 6290 Planarity : 0.005 0.050 7837 Dihedral : 6.503 86.987 5928 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 1.48 % Allowed : 10.31 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.11), residues: 5355 helix: -1.40 (0.12), residues: 1632 sheet: 0.35 (0.15), residues: 1139 loop : -1.17 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP S 165 HIS 0.007 0.001 HIS U 285 PHE 0.011 0.001 PHE G 59 TYR 0.023 0.001 TYR J 316 ARG 0.004 0.001 ARG I 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 436 time to evaluate : 4.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 ARG cc_start: 0.7767 (mmt90) cc_final: 0.6151 (ptt180) REVERT: B 174 MET cc_start: 0.9129 (tpp) cc_final: 0.8846 (tpt) REVERT: F 132 ARG cc_start: 0.7662 (ttt-90) cc_final: 0.6468 (ptt180) REVERT: G 123 ASP cc_start: 0.7488 (m-30) cc_final: 0.7287 (m-30) REVERT: H 211 MET cc_start: 0.8742 (ttt) cc_final: 0.8445 (ttp) REVERT: I 255 MET cc_start: 0.7277 (tpp) cc_final: 0.6831 (tpp) REVERT: J 255 MET cc_start: 0.7729 (tpp) cc_final: 0.7331 (tpp) REVERT: K 125 ILE cc_start: 0.9183 (mt) cc_final: 0.8900 (mm) REVERT: K 152 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.7075 (p90) REVERT: L 123 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8327 (p0) REVERT: L 220 MET cc_start: 0.8942 (mmt) cc_final: 0.7933 (mpp) REVERT: M 180 ASN cc_start: 0.8362 (t0) cc_final: 0.8065 (t0) REVERT: M 255 MET cc_start: 0.7283 (tpp) cc_final: 0.6990 (tpp) REVERT: N 117 TRP cc_start: 0.8927 (m100) cc_final: 0.8511 (m100) REVERT: N 226 LEU cc_start: 0.8979 (mm) cc_final: 0.8602 (tp) REVERT: N 255 MET cc_start: 0.6358 (mmt) cc_final: 0.5831 (tpt) REVERT: N 281 ASP cc_start: 0.8561 (t0) cc_final: 0.8087 (t70) REVERT: O 125 ILE cc_start: 0.9352 (mt) cc_final: 0.9135 (mm) REVERT: O 149 MET cc_start: 0.9126 (tpp) cc_final: 0.8791 (tpp) REVERT: O 180 ASN cc_start: 0.8752 (t0) cc_final: 0.8442 (t0) REVERT: Q 255 MET cc_start: 0.7067 (tpp) cc_final: 0.6369 (tpp) REVERT: R 125 ILE cc_start: 0.9040 (mt) cc_final: 0.8836 (mm) REVERT: R 138 ARG cc_start: 0.9037 (mtp85) cc_final: 0.8823 (mtt180) REVERT: S 207 THR cc_start: 0.9557 (p) cc_final: 0.9325 (p) REVERT: S 255 MET cc_start: 0.7665 (tpp) cc_final: 0.6920 (tpp) REVERT: U 132 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.6126 (ttp-170) REVERT: U 166 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7252 (mt-10) REVERT: U 199 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8150 (ttm-80) REVERT: U 234 PHE cc_start: 0.8763 (t80) cc_final: 0.8338 (t80) REVERT: U 281 ASP cc_start: 0.7933 (t0) cc_final: 0.7428 (t0) outliers start: 68 outliers final: 26 residues processed: 489 average time/residue: 0.5903 time to fit residues: 488.0820 Evaluate side-chains 382 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 353 time to evaluate : 4.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain L residue 123 ASP Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 318 ASP Chi-restraints excluded: chain N residue 307 ASN Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 265 TYR Chi-restraints excluded: chain U residue 305 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 265 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 398 optimal weight: 8.9990 chunk 325 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 479 optimal weight: 6.9990 chunk 517 optimal weight: 9.9990 chunk 426 optimal weight: 10.0000 chunk 475 optimal weight: 0.3980 chunk 163 optimal weight: 0.0870 chunk 384 optimal weight: 8.9990 overall best weight: 4.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 ASN D 177 ASN F 86 GLN ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 GLN H 119 ASN I 184 HIS I 228 GLN ** J 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 294 ASN L 294 ASN L 307 ASN O 86 GLN P 119 ASN P 308 HIS Q 180 ASN Q 307 ASN U 285 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 44149 Z= 0.355 Angle : 0.652 16.766 59959 Z= 0.344 Chirality : 0.045 0.223 6290 Planarity : 0.005 0.071 7837 Dihedral : 6.204 89.476 5903 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.51 % Favored : 94.47 % Rotamer: Outliers : 2.53 % Allowed : 11.72 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.11), residues: 5355 helix: -1.16 (0.12), residues: 1632 sheet: 0.17 (0.15), residues: 1139 loop : -1.35 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 165 HIS 0.007 0.001 HIS U 285 PHE 0.022 0.002 PHE D 118 TYR 0.016 0.002 TYR G 65 ARG 0.011 0.001 ARG F 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 353 time to evaluate : 5.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 132 ARG cc_start: 0.7915 (mmt90) cc_final: 0.6112 (ptt180) REVERT: B 255 MET cc_start: 0.6850 (tpt) cc_final: 0.6437 (tpp) REVERT: B 280 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8677 (tt) REVERT: F 132 ARG cc_start: 0.7704 (ttt-90) cc_final: 0.6426 (ptt180) REVERT: G 181 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8215 (tp30) REVERT: H 211 MET cc_start: 0.8865 (ttt) cc_final: 0.8624 (ttp) REVERT: I 123 ASP cc_start: 0.8004 (p0) cc_final: 0.7671 (p0) REVERT: I 255 MET cc_start: 0.7674 (tpp) cc_final: 0.7345 (tpp) REVERT: J 255 MET cc_start: 0.7721 (tpp) cc_final: 0.7310 (tpp) REVERT: K 125 ILE cc_start: 0.9299 (mt) cc_final: 0.9062 (mp) REVERT: K 152 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.7392 (p90) REVERT: L 220 MET cc_start: 0.8997 (mmt) cc_final: 0.8088 (mpp) REVERT: M 174 MET cc_start: 0.9169 (tpp) cc_final: 0.8809 (tpp) REVERT: N 117 TRP cc_start: 0.9135 (m100) cc_final: 0.8413 (m100) REVERT: N 223 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8547 (pmm) REVERT: N 281 ASP cc_start: 0.8778 (t0) cc_final: 0.8315 (t70) REVERT: O 180 ASN cc_start: 0.8886 (t0) cc_final: 0.8573 (t0) REVERT: P 129 ARG cc_start: 0.8184 (mtm180) cc_final: 0.7961 (mtp85) REVERT: P 255 MET cc_start: 0.6063 (mmt) cc_final: 0.5110 (tpt) REVERT: Q 163 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7598 (mtp) REVERT: Q 211 MET cc_start: 0.8142 (ptm) cc_final: 0.7760 (ptm) REVERT: Q 255 MET cc_start: 0.7116 (tpp) cc_final: 0.6426 (tpp) REVERT: R 96 GLU cc_start: 0.6840 (pp20) cc_final: 0.6586 (pp20) REVERT: R 123 ASP cc_start: 0.8967 (p0) cc_final: 0.8545 (p0) REVERT: S 180 ASN cc_start: 0.8581 (t0) cc_final: 0.8358 (t0) REVERT: S 255 MET cc_start: 0.7778 (tpp) cc_final: 0.7166 (tpp) REVERT: U 100 CYS cc_start: 0.8775 (t) cc_final: 0.8542 (t) REVERT: U 132 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.5979 (ttp-170) REVERT: U 166 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7495 (mt-10) REVERT: U 234 PHE cc_start: 0.8971 (t80) cc_final: 0.8543 (t80) outliers start: 116 outliers final: 78 residues processed: 443 average time/residue: 0.4923 time to fit residues: 373.9607 Evaluate side-chains 415 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 332 time to evaluate : 3.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 306 LEU Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 165 TRP Chi-restraints excluded: chain K residue 274 ILE Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 307 ASN Chi-restraints excluded: chain M residue 30 CYS Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 318 ASP Chi-restraints excluded: chain N residue 223 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain N residue 307 ASN Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 100 CYS Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 308 HIS Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain Q residue 163 MET Chi-restraints excluded: chain Q residue 303 VAL Chi-restraints excluded: chain Q residue 308 HIS Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 143 ASP Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 172 ASP Chi-restraints excluded: chain S residue 220 MET Chi-restraints excluded: chain S residue 296 ASN Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain U residue 90 GLU Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 163 MET Chi-restraints excluded: chain U residue 220 MET Chi-restraints excluded: chain U residue 265 TYR Chi-restraints excluded: chain U residue 305 HIS Chi-restraints excluded: chain U residue 308 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 473 optimal weight: 9.9990 chunk 360 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 321 optimal weight: 6.9990 chunk 481 optimal weight: 0.5980 chunk 509 optimal weight: 6.9990 chunk 251 optimal weight: 4.9990 chunk 456 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 HIS D 39 ASN F 119 ASN I 177 ASN ** J 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 294 ASN L 294 ASN L 307 ASN O 168 GLN Q 62 HIS Q 307 ASN U 285 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 44149 Z= 0.218 Angle : 0.576 16.803 59959 Z= 0.298 Chirality : 0.043 0.220 6290 Planarity : 0.005 0.058 7837 Dihedral : 5.910 87.715 5901 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.91 % Favored : 95.07 % Rotamer: Outliers : 2.59 % Allowed : 12.72 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.11), residues: 5355 helix: -0.95 (0.13), residues: 1632 sheet: 0.19 (0.15), residues: 1139 loop : -1.37 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 165 HIS 0.021 0.001 HIS P 308 PHE 0.017 0.001 PHE D 118 TYR 0.022 0.001 TYR J 201 ARG 0.008 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 344 time to evaluate : 5.001 Fit side-chains revert: symmetry clash REVERT: B 132 ARG cc_start: 0.8005 (mmt90) cc_final: 0.6010 (ptp-170) REVERT: B 280 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8655 (tt) REVERT: F 100 CYS cc_start: 0.8911 (t) cc_final: 0.8449 (t) REVERT: F 132 ARG cc_start: 0.7530 (ttt-90) cc_final: 0.6293 (ptt180) REVERT: I 123 ASP cc_start: 0.8018 (p0) cc_final: 0.7673 (p0) REVERT: I 255 MET cc_start: 0.7584 (tpp) cc_final: 0.7280 (tpp) REVERT: J 255 MET cc_start: 0.7748 (tpp) cc_final: 0.7430 (tpp) REVERT: K 125 ILE cc_start: 0.9267 (mt) cc_final: 0.9019 (mp) REVERT: K 152 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.7323 (p90) REVERT: L 176 MET cc_start: 0.8709 (tpp) cc_final: 0.8402 (tpt) REVERT: L 220 MET cc_start: 0.9061 (mmt) cc_final: 0.8272 (mpp) REVERT: M 255 MET cc_start: 0.8069 (tpp) cc_final: 0.7514 (tpp) REVERT: N 117 TRP cc_start: 0.9076 (m100) cc_final: 0.8516 (m100) REVERT: N 223 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8507 (pmm) REVERT: N 255 MET cc_start: 0.6172 (mmt) cc_final: 0.5667 (tpt) REVERT: O 125 ILE cc_start: 0.9369 (mt) cc_final: 0.9120 (mp) REVERT: O 163 MET cc_start: 0.7755 (mtp) cc_final: 0.7411 (mtp) REVERT: O 166 GLU cc_start: 0.8238 (mp0) cc_final: 0.7988 (mp0) REVERT: O 180 ASN cc_start: 0.8751 (t0) cc_final: 0.8415 (t0) REVERT: P 255 MET cc_start: 0.6079 (mmt) cc_final: 0.5571 (mmt) REVERT: P 265 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.6715 (p90) REVERT: Q 255 MET cc_start: 0.7139 (tpp) cc_final: 0.6526 (tpp) REVERT: R 86 GLN cc_start: 0.7292 (tt0) cc_final: 0.7012 (tt0) REVERT: R 96 GLU cc_start: 0.6824 (pp20) cc_final: 0.6464 (pp20) REVERT: R 123 ASP cc_start: 0.8973 (p0) cc_final: 0.8573 (p0) REVERT: S 180 ASN cc_start: 0.8430 (t0) cc_final: 0.8205 (t0) REVERT: S 255 MET cc_start: 0.7762 (tpp) cc_final: 0.7173 (tpp) REVERT: U 100 CYS cc_start: 0.8688 (t) cc_final: 0.8259 (t) REVERT: U 132 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.6036 (ttp-170) REVERT: U 166 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7411 (mt-10) REVERT: U 234 PHE cc_start: 0.8974 (t80) cc_final: 0.8531 (t80) REVERT: U 278 TYR cc_start: 0.8438 (t80) cc_final: 0.8148 (m-80) outliers start: 119 outliers final: 73 residues processed: 431 average time/residue: 0.5490 time to fit residues: 409.9464 Evaluate side-chains 409 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 331 time to evaluate : 5.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 293 MET Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 274 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 307 ASN Chi-restraints excluded: chain M residue 30 CYS Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 163 MET Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 318 ASP Chi-restraints excluded: chain N residue 223 MET Chi-restraints excluded: chain N residue 307 ASN Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 100 CYS Chi-restraints excluded: chain P residue 265 TYR Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain Q residue 308 HIS Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 269 ASP Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 143 ASP Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 172 ASP Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 163 MET Chi-restraints excluded: chain U residue 220 MET Chi-restraints excluded: chain U residue 265 TYR Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 305 HIS Chi-restraints excluded: chain U residue 308 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 424 optimal weight: 10.0000 chunk 289 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 379 optimal weight: 6.9990 chunk 210 optimal weight: 0.0020 chunk 434 optimal weight: 4.9990 chunk 352 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 chunk 457 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 overall best weight: 3.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 294 ASN L 294 ASN ** L 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 HIS P 308 HIS S 296 ASN U 228 GLN U 285 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 44149 Z= 0.265 Angle : 0.581 17.175 59959 Z= 0.301 Chirality : 0.043 0.220 6290 Planarity : 0.005 0.056 7837 Dihedral : 5.881 87.624 5901 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.96 % Favored : 94.02 % Rotamer: Outliers : 3.07 % Allowed : 12.98 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.11), residues: 5355 helix: -0.83 (0.13), residues: 1615 sheet: 0.14 (0.15), residues: 1139 loop : -1.49 (0.11), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 165 HIS 0.008 0.001 HIS U 285 PHE 0.016 0.001 PHE D 118 TYR 0.013 0.001 TYR G 65 ARG 0.006 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 341 time to evaluate : 4.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 132 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.5944 (ptp-170) REVERT: B 280 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8656 (tt) REVERT: F 132 ARG cc_start: 0.7549 (ttt-90) cc_final: 0.6257 (ptt180) REVERT: F 255 MET cc_start: 0.8310 (mmm) cc_final: 0.7995 (tpt) REVERT: G 123 ASP cc_start: 0.8190 (p0) cc_final: 0.7890 (m-30) REVERT: I 123 ASP cc_start: 0.8028 (p0) cc_final: 0.7681 (p0) REVERT: I 255 MET cc_start: 0.7681 (tpp) cc_final: 0.7374 (tpp) REVERT: J 255 MET cc_start: 0.7729 (tpp) cc_final: 0.7514 (tpp) REVERT: J 281 ASP cc_start: 0.8944 (t0) cc_final: 0.8672 (t0) REVERT: K 152 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7372 (p90) REVERT: K 220 MET cc_start: 0.7813 (mtt) cc_final: 0.7599 (mmt) REVERT: L 176 MET cc_start: 0.8785 (tpp) cc_final: 0.8357 (tpt) REVERT: L 220 MET cc_start: 0.9015 (mmt) cc_final: 0.8369 (mpp) REVERT: M 255 MET cc_start: 0.7984 (tpp) cc_final: 0.7435 (tpp) REVERT: N 117 TRP cc_start: 0.9098 (m100) cc_final: 0.8450 (m100) REVERT: N 223 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8628 (ptt) REVERT: N 255 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5801 (tpp) REVERT: O 163 MET cc_start: 0.7858 (mtp) cc_final: 0.7413 (mtp) REVERT: O 166 GLU cc_start: 0.8299 (mp0) cc_final: 0.8009 (mp0) REVERT: P 255 MET cc_start: 0.6051 (mmt) cc_final: 0.5518 (mmt) REVERT: P 265 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.6723 (p90) REVERT: Q 211 MET cc_start: 0.8138 (ptm) cc_final: 0.7741 (ptm) REVERT: Q 255 MET cc_start: 0.7128 (tpp) cc_final: 0.6544 (tpp) REVERT: R 86 GLN cc_start: 0.7336 (tt0) cc_final: 0.6973 (tt0) REVERT: R 96 GLU cc_start: 0.6785 (pp20) cc_final: 0.6409 (pp20) REVERT: R 123 ASP cc_start: 0.9022 (p0) cc_final: 0.8602 (p0) REVERT: S 180 ASN cc_start: 0.8455 (t0) cc_final: 0.8241 (t0) REVERT: U 100 CYS cc_start: 0.8711 (t) cc_final: 0.8337 (t) REVERT: U 132 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.6089 (ttp-170) REVERT: U 234 PHE cc_start: 0.8997 (t80) cc_final: 0.8577 (t80) REVERT: U 278 TYR cc_start: 0.8470 (t80) cc_final: 0.8147 (m-80) outliers start: 141 outliers final: 102 residues processed: 443 average time/residue: 0.5021 time to fit residues: 383.8580 Evaluate side-chains 436 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 327 time to evaluate : 5.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 223 MET Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 293 MET Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 274 ILE Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 307 ASN Chi-restraints excluded: chain M residue 30 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 134 SER Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 163 MET Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 318 ASP Chi-restraints excluded: chain N residue 223 MET Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 293 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain N residue 307 ASN Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 100 CYS Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 194 ASP Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 265 TYR Chi-restraints excluded: chain P residue 308 HIS Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain Q residue 308 HIS Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 143 ASP Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 163 MET Chi-restraints excluded: chain S residue 165 TRP Chi-restraints excluded: chain S residue 172 ASP Chi-restraints excluded: chain S residue 220 MET Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain U residue 90 GLU Chi-restraints excluded: chain U residue 97 THR Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 163 MET Chi-restraints excluded: chain U residue 220 MET Chi-restraints excluded: chain U residue 228 GLN Chi-restraints excluded: chain U residue 265 TYR Chi-restraints excluded: chain U residue 280 ILE Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 305 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 171 optimal weight: 8.9990 chunk 458 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 299 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 509 optimal weight: 5.9990 chunk 423 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 298 GLN K 294 ASN L 294 ASN P 184 HIS P 308 HIS U 228 GLN U 285 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 44149 Z= 0.339 Angle : 0.615 17.434 59959 Z= 0.319 Chirality : 0.044 0.220 6290 Planarity : 0.005 0.060 7837 Dihedral : 6.010 89.113 5901 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.42 % Favored : 93.56 % Rotamer: Outliers : 3.42 % Allowed : 13.53 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.11), residues: 5355 helix: -0.80 (0.13), residues: 1598 sheet: -0.08 (0.15), residues: 1173 loop : -1.55 (0.11), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 165 HIS 0.008 0.001 HIS U 285 PHE 0.018 0.001 PHE D 118 TYR 0.015 0.001 TYR J 201 ARG 0.009 0.000 ARG U 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 332 time to evaluate : 5.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 132 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.5788 (ptp-170) REVERT: B 280 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8666 (tt) REVERT: D 123 ASP cc_start: 0.9005 (p0) cc_final: 0.8656 (p0) REVERT: F 132 ARG cc_start: 0.7585 (ttt-90) cc_final: 0.6259 (ptt180) REVERT: F 226 LEU cc_start: 0.8953 (mm) cc_final: 0.8727 (mp) REVERT: G 123 ASP cc_start: 0.8239 (p0) cc_final: 0.7908 (m-30) REVERT: I 123 ASP cc_start: 0.8117 (p0) cc_final: 0.7746 (p0) REVERT: I 207 THR cc_start: 0.9589 (p) cc_final: 0.9384 (p) REVERT: I 216 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.7436 (p90) REVERT: J 223 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7283 (ptm) REVERT: J 255 MET cc_start: 0.7713 (tpp) cc_final: 0.7510 (tpp) REVERT: K 152 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.7486 (p90) REVERT: K 220 MET cc_start: 0.7804 (mtt) cc_final: 0.7526 (mmt) REVERT: L 176 MET cc_start: 0.8795 (tpp) cc_final: 0.8425 (tpt) REVERT: L 220 MET cc_start: 0.9044 (mmt) cc_final: 0.8492 (mpp) REVERT: M 255 MET cc_start: 0.7989 (tpp) cc_final: 0.7659 (tpp) REVERT: N 181 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7423 (tt0) REVERT: N 255 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.5630 (tpp) REVERT: O 163 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7440 (mtp) REVERT: O 166 GLU cc_start: 0.8272 (mp0) cc_final: 0.7970 (mp0) REVERT: P 255 MET cc_start: 0.5904 (mmt) cc_final: 0.5364 (mmt) REVERT: P 265 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6609 (p90) REVERT: P 309 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6757 (pp30) REVERT: Q 211 MET cc_start: 0.8110 (ptm) cc_final: 0.7711 (ptm) REVERT: Q 255 MET cc_start: 0.7171 (tpp) cc_final: 0.6575 (tpp) REVERT: R 86 GLN cc_start: 0.7371 (tt0) cc_final: 0.7030 (tt0) REVERT: U 100 CYS cc_start: 0.8787 (t) cc_final: 0.8429 (t) REVERT: U 132 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.6259 (ttp-170) REVERT: U 234 PHE cc_start: 0.9019 (t80) cc_final: 0.8622 (t80) REVERT: U 278 TYR cc_start: 0.8505 (t80) cc_final: 0.8165 (m-80) outliers start: 157 outliers final: 118 residues processed: 450 average time/residue: 0.5396 time to fit residues: 422.0939 Evaluate side-chains 444 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 316 time to evaluate : 5.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 223 MET Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 293 MET Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain K residue 274 ILE Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 303 VAL Chi-restraints excluded: chain M residue 30 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 134 SER Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 318 ASP Chi-restraints excluded: chain N residue 80 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 293 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain N residue 307 ASN Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 30 CYS Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 100 CYS Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 194 ASP Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 265 TYR Chi-restraints excluded: chain P residue 308 HIS Chi-restraints excluded: chain P residue 309 GLN Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 62 HIS Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain Q residue 163 MET Chi-restraints excluded: chain Q residue 165 TRP Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain Q residue 303 VAL Chi-restraints excluded: chain Q residue 308 HIS Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 143 ASP Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 163 MET Chi-restraints excluded: chain S residue 165 TRP Chi-restraints excluded: chain S residue 220 MET Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain U residue 90 GLU Chi-restraints excluded: chain U residue 97 THR Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 163 MET Chi-restraints excluded: chain U residue 220 MET Chi-restraints excluded: chain U residue 265 TYR Chi-restraints excluded: chain U residue 280 ILE Chi-restraints excluded: chain U residue 285 HIS Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 305 HIS Chi-restraints excluded: chain U residue 308 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 491 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 290 optimal weight: 5.9990 chunk 372 optimal weight: 10.0000 chunk 288 optimal weight: 2.9990 chunk 429 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 507 optimal weight: 1.9990 chunk 317 optimal weight: 0.4980 chunk 309 optimal weight: 0.4980 chunk 234 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 298 GLN P 71 HIS P 184 HIS P 308 HIS ** Q 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 44149 Z= 0.185 Angle : 0.556 17.226 59959 Z= 0.284 Chirality : 0.042 0.219 6290 Planarity : 0.004 0.050 7837 Dihedral : 5.720 88.222 5901 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.40 % Favored : 94.58 % Rotamer: Outliers : 2.81 % Allowed : 14.29 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.11), residues: 5355 helix: -0.64 (0.13), residues: 1598 sheet: 0.06 (0.16), residues: 1071 loop : -1.61 (0.11), residues: 2686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 117 HIS 0.013 0.001 HIS U 285 PHE 0.014 0.001 PHE D 118 TYR 0.012 0.001 TYR G 65 ARG 0.004 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 336 time to evaluate : 5.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 132 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.5755 (ptp-170) REVERT: B 280 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8619 (tt) REVERT: D 181 GLU cc_start: 0.7354 (tt0) cc_final: 0.7106 (tt0) REVERT: F 100 CYS cc_start: 0.9020 (t) cc_final: 0.8377 (t) REVERT: F 132 ARG cc_start: 0.7532 (ttt-90) cc_final: 0.6234 (ptt180) REVERT: F 226 LEU cc_start: 0.8934 (mm) cc_final: 0.8689 (mp) REVERT: G 123 ASP cc_start: 0.8277 (p0) cc_final: 0.7971 (m-30) REVERT: G 152 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.7140 (p90) REVERT: I 4 ILE cc_start: 0.8761 (mm) cc_final: 0.8524 (mt) REVERT: I 123 ASP cc_start: 0.8080 (p0) cc_final: 0.7719 (p0) REVERT: I 194 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8263 (p0) REVERT: I 216 TYR cc_start: 0.7598 (OUTLIER) cc_final: 0.7329 (p90) REVERT: I 255 MET cc_start: 0.7715 (tpp) cc_final: 0.7324 (tpp) REVERT: J 255 MET cc_start: 0.7688 (tpp) cc_final: 0.7370 (tpp) REVERT: K 152 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.7454 (p90) REVERT: K 220 MET cc_start: 0.7809 (mtt) cc_final: 0.7502 (mmt) REVERT: L 220 MET cc_start: 0.9047 (mmt) cc_final: 0.8505 (mpp) REVERT: M 255 MET cc_start: 0.7933 (tpp) cc_final: 0.7624 (tpp) REVERT: N 117 TRP cc_start: 0.9104 (m100) cc_final: 0.8469 (m100) REVERT: N 255 MET cc_start: 0.6070 (OUTLIER) cc_final: 0.5598 (tpt) REVERT: O 163 MET cc_start: 0.8000 (mtp) cc_final: 0.7463 (mtp) REVERT: O 166 GLU cc_start: 0.8288 (mp0) cc_final: 0.8010 (mp0) REVERT: P 255 MET cc_start: 0.6082 (mmt) cc_final: 0.5121 (tpt) REVERT: P 309 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6930 (pp30) REVERT: Q 59 PHE cc_start: 0.8549 (m-80) cc_final: 0.8218 (m-80) REVERT: Q 255 MET cc_start: 0.7087 (tpp) cc_final: 0.6510 (tpp) REVERT: R 86 GLN cc_start: 0.7315 (tt0) cc_final: 0.6973 (tt0) REVERT: R 96 GLU cc_start: 0.6723 (pp20) cc_final: 0.6392 (pp20) REVERT: U 100 CYS cc_start: 0.8677 (t) cc_final: 0.8216 (t) REVERT: U 132 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.6273 (ttp-170) REVERT: U 234 PHE cc_start: 0.8933 (t80) cc_final: 0.8576 (t80) outliers start: 129 outliers final: 95 residues processed: 430 average time/residue: 0.4991 time to fit residues: 371.9497 Evaluate side-chains 428 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 324 time to evaluate : 4.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 293 MET Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain K residue 274 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 319 ILE Chi-restraints excluded: chain M residue 30 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 134 SER Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 163 MET Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 318 ASP Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain N residue 307 ASN Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 30 CYS Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 194 ASP Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain O residue 293 MET Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 194 ASP Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 309 GLN Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 165 TRP Chi-restraints excluded: chain S residue 220 MET Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain U residue 90 GLU Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 163 MET Chi-restraints excluded: chain U residue 220 MET Chi-restraints excluded: chain U residue 265 TYR Chi-restraints excluded: chain U residue 280 ILE Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 305 HIS Chi-restraints excluded: chain U residue 308 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 314 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 303 optimal weight: 10.0000 chunk 153 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 346 optimal weight: 0.6980 chunk 251 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 399 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 39 ASN P 184 HIS ** Q 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 182 GLN Q 307 ASN S 180 ASN U 285 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 44149 Z= 0.145 Angle : 0.533 17.287 59959 Z= 0.269 Chirality : 0.042 0.215 6290 Planarity : 0.004 0.048 7837 Dihedral : 5.364 85.985 5901 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.87 % Favored : 95.11 % Rotamer: Outliers : 2.42 % Allowed : 14.92 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.11), residues: 5355 helix: -0.52 (0.13), residues: 1598 sheet: 0.12 (0.15), residues: 1173 loop : -1.51 (0.11), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 117 HIS 0.008 0.001 HIS U 285 PHE 0.011 0.001 PHE D 118 TYR 0.021 0.001 TYR J 201 ARG 0.004 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 361 time to evaluate : 5.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.5714 (ptp-170) REVERT: B 174 MET cc_start: 0.9148 (tpp) cc_final: 0.8826 (tpt) REVERT: B 280 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8634 (tt) REVERT: D 174 MET cc_start: 0.9191 (tpp) cc_final: 0.8862 (tpp) REVERT: F 132 ARG cc_start: 0.7597 (ttt-90) cc_final: 0.6236 (ptt180) REVERT: F 226 LEU cc_start: 0.8926 (mm) cc_final: 0.8710 (mp) REVERT: G 123 ASP cc_start: 0.8245 (p0) cc_final: 0.7999 (m-30) REVERT: G 148 MET cc_start: 0.8795 (mtp) cc_final: 0.8591 (mtt) REVERT: G 152 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7074 (p90) REVERT: G 207 THR cc_start: 0.9538 (p) cc_final: 0.9327 (p) REVERT: I 4 ILE cc_start: 0.8672 (mm) cc_final: 0.8422 (mt) REVERT: I 194 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8220 (p0) REVERT: I 216 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.7328 (p90) REVERT: I 255 MET cc_start: 0.7619 (tpp) cc_final: 0.7256 (tpp) REVERT: J 255 MET cc_start: 0.7675 (tpp) cc_final: 0.7370 (tpp) REVERT: K 119 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8661 (p0) REVERT: K 152 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7359 (p90) REVERT: K 220 MET cc_start: 0.7845 (mtt) cc_final: 0.7533 (mmt) REVERT: L 123 ASP cc_start: 0.8774 (p0) cc_final: 0.8468 (p0) REVERT: L 220 MET cc_start: 0.9041 (mmt) cc_final: 0.8242 (mpp) REVERT: M 255 MET cc_start: 0.7814 (tpp) cc_final: 0.7518 (tpp) REVERT: N 117 TRP cc_start: 0.9021 (m100) cc_final: 0.8401 (m100) REVERT: N 255 MET cc_start: 0.6289 (OUTLIER) cc_final: 0.5877 (tpt) REVERT: O 163 MET cc_start: 0.8019 (mtp) cc_final: 0.7477 (mtp) REVERT: O 166 GLU cc_start: 0.8221 (mp0) cc_final: 0.7959 (mp0) REVERT: O 180 ASN cc_start: 0.8680 (t0) cc_final: 0.8366 (t0) REVERT: P 255 MET cc_start: 0.6073 (mmt) cc_final: 0.5307 (tpt) REVERT: P 309 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6714 (pp30) REVERT: Q 59 PHE cc_start: 0.8510 (m-80) cc_final: 0.8143 (m-80) REVERT: Q 255 MET cc_start: 0.6980 (tpp) cc_final: 0.6440 (tpp) REVERT: R 86 GLN cc_start: 0.7305 (tt0) cc_final: 0.6970 (tt0) REVERT: R 96 GLU cc_start: 0.6697 (pp20) cc_final: 0.6381 (pp20) REVERT: U 100 CYS cc_start: 0.8580 (t) cc_final: 0.7925 (t) REVERT: U 132 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.6331 (ttp-170) REVERT: U 176 MET cc_start: 0.9310 (tpp) cc_final: 0.9078 (tpp) REVERT: U 234 PHE cc_start: 0.8883 (t80) cc_final: 0.8582 (t80) outliers start: 111 outliers final: 77 residues processed: 444 average time/residue: 0.5059 time to fit residues: 389.2312 Evaluate side-chains 431 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 344 time to evaluate : 5.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 293 MET Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 303 VAL Chi-restraints excluded: chain L residue 319 ILE Chi-restraints excluded: chain M residue 30 CYS Chi-restraints excluded: chain M residue 134 SER Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 163 MET Chi-restraints excluded: chain M residue 235 GLU Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain N residue 80 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain N residue 307 ASN Chi-restraints excluded: chain O residue 30 CYS Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain O residue 293 MET Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 194 ASP Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 309 GLN Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 165 TRP Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain U residue 90 GLU Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 163 MET Chi-restraints excluded: chain U residue 220 MET Chi-restraints excluded: chain U residue 265 TYR Chi-restraints excluded: chain U residue 280 ILE Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 305 HIS Chi-restraints excluded: chain U residue 308 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 462 optimal weight: 8.9990 chunk 486 optimal weight: 10.0000 chunk 443 optimal weight: 10.0000 chunk 473 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 371 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 427 optimal weight: 9.9990 chunk 447 optimal weight: 2.9990 chunk 471 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 GLN I 177 ASN K 180 ASN O 39 ASN ** Q 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 285 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 44149 Z= 0.296 Angle : 0.594 17.528 59959 Z= 0.304 Chirality : 0.043 0.210 6290 Planarity : 0.004 0.050 7837 Dihedral : 5.637 87.353 5901 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.52 % Favored : 93.46 % Rotamer: Outliers : 2.70 % Allowed : 15.01 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.11), residues: 5355 helix: -0.46 (0.13), residues: 1564 sheet: 0.01 (0.15), residues: 1173 loop : -1.61 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 165 HIS 0.008 0.001 HIS U 285 PHE 0.018 0.001 PHE D 118 TYR 0.023 0.001 TYR J 201 ARG 0.010 0.000 ARG J 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 337 time to evaluate : 5.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.5747 (ptp-170) REVERT: B 280 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8656 (tt) REVERT: F 132 ARG cc_start: 0.7696 (ttt-90) cc_final: 0.6298 (ptt180) REVERT: F 226 LEU cc_start: 0.8963 (mm) cc_final: 0.8749 (mp) REVERT: G 123 ASP cc_start: 0.8305 (p0) cc_final: 0.8004 (m-30) REVERT: G 152 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7326 (p90) REVERT: I 123 ASP cc_start: 0.8099 (p0) cc_final: 0.7737 (p0) REVERT: I 216 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7468 (p90) REVERT: I 255 MET cc_start: 0.7850 (tpp) cc_final: 0.7423 (tpp) REVERT: J 255 MET cc_start: 0.7732 (tpp) cc_final: 0.7515 (tpp) REVERT: K 119 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8821 (p0) REVERT: K 152 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.7452 (p90) REVERT: K 220 MET cc_start: 0.7829 (mtt) cc_final: 0.7504 (mmt) REVERT: L 123 ASP cc_start: 0.8806 (p0) cc_final: 0.8544 (p0) REVERT: L 220 MET cc_start: 0.8996 (mmt) cc_final: 0.8185 (mpp) REVERT: M 255 MET cc_start: 0.7890 (tpp) cc_final: 0.7569 (tpp) REVERT: N 255 MET cc_start: 0.6234 (OUTLIER) cc_final: 0.5705 (tpt) REVERT: O 163 MET cc_start: 0.8048 (mtp) cc_final: 0.7403 (mtp) REVERT: O 166 GLU cc_start: 0.8314 (mp0) cc_final: 0.7963 (mp0) REVERT: O 180 ASN cc_start: 0.8768 (t0) cc_final: 0.8450 (t0) REVERT: P 90 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7439 (tm-30) REVERT: P 255 MET cc_start: 0.5992 (mmt) cc_final: 0.5087 (tpt) REVERT: P 309 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6707 (pp30) REVERT: Q 59 PHE cc_start: 0.8572 (m-80) cc_final: 0.8215 (m-80) REVERT: Q 123 ASP cc_start: 0.8237 (p0) cc_final: 0.7960 (p0) REVERT: Q 255 MET cc_start: 0.7067 (tpp) cc_final: 0.6516 (tpp) REVERT: R 86 GLN cc_start: 0.7422 (tt0) cc_final: 0.7053 (tt0) REVERT: S 166 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7332 (mt-10) REVERT: S 219 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7656 (pp20) REVERT: U 100 CYS cc_start: 0.8727 (t) cc_final: 0.8332 (t) REVERT: U 132 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.6348 (ttp-170) REVERT: U 234 PHE cc_start: 0.8976 (t80) cc_final: 0.8652 (t80) outliers start: 124 outliers final: 98 residues processed: 430 average time/residue: 0.5018 time to fit residues: 374.4613 Evaluate side-chains 433 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 325 time to evaluate : 5.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 147 SER Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 293 MET Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 180 ASN Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 303 VAL Chi-restraints excluded: chain L residue 319 ILE Chi-restraints excluded: chain M residue 30 CYS Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 134 SER Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 163 MET Chi-restraints excluded: chain M residue 235 GLU Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain N residue 80 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain N residue 307 ASN Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 30 CYS Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 194 ASP Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 309 GLN Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 62 HIS Chi-restraints excluded: chain Q residue 134 SER Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain Q residue 308 HIS Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 163 MET Chi-restraints excluded: chain S residue 165 TRP Chi-restraints excluded: chain S residue 219 GLU Chi-restraints excluded: chain S residue 220 MET Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain U residue 90 GLU Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 163 MET Chi-restraints excluded: chain U residue 220 MET Chi-restraints excluded: chain U residue 265 TYR Chi-restraints excluded: chain U residue 280 ILE Chi-restraints excluded: chain U residue 285 HIS Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 305 HIS Chi-restraints excluded: chain U residue 308 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 310 optimal weight: 0.8980 chunk 500 optimal weight: 1.9990 chunk 305 optimal weight: 0.0870 chunk 237 optimal weight: 4.9990 chunk 347 optimal weight: 0.8980 chunk 525 optimal weight: 0.5980 chunk 483 optimal weight: 4.9990 chunk 418 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 322 optimal weight: 0.6980 chunk 256 optimal weight: 6.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 180 ASN O 39 ASN P 184 HIS ** Q 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 177 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 44149 Z= 0.228 Angle : 0.688 59.199 59959 Z= 0.380 Chirality : 0.047 1.571 6290 Planarity : 0.005 0.195 7837 Dihedral : 5.638 87.374 5901 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.35 % Favored : 93.61 % Rotamer: Outliers : 2.72 % Allowed : 15.14 % Favored : 82.14 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.11), residues: 5355 helix: -0.43 (0.13), residues: 1564 sheet: -0.01 (0.15), residues: 1173 loop : -1.61 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 165 HIS 0.323 0.002 HIS U 285 PHE 0.016 0.001 PHE D 118 TYR 0.021 0.001 TYR J 201 ARG 0.003 0.000 ARG D 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 326 time to evaluate : 5.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 132 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.5733 (ptp-170) REVERT: B 280 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8658 (tt) REVERT: F 132 ARG cc_start: 0.7683 (ttt-90) cc_final: 0.6297 (ptt180) REVERT: F 226 LEU cc_start: 0.8955 (mm) cc_final: 0.8732 (mp) REVERT: G 123 ASP cc_start: 0.8296 (p0) cc_final: 0.7995 (m-30) REVERT: G 152 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.7378 (p90) REVERT: I 123 ASP cc_start: 0.8089 (p0) cc_final: 0.7725 (p0) REVERT: I 165 TRP cc_start: 0.9030 (OUTLIER) cc_final: 0.8569 (m-10) REVERT: I 216 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7475 (p90) REVERT: I 255 MET cc_start: 0.7846 (tpp) cc_final: 0.7418 (tpp) REVERT: J 255 MET cc_start: 0.7727 (tpp) cc_final: 0.7513 (tpp) REVERT: K 119 ASN cc_start: 0.9046 (OUTLIER) cc_final: 0.8815 (p0) REVERT: K 152 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.7444 (p90) REVERT: K 180 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8317 (t0) REVERT: K 220 MET cc_start: 0.7825 (mtt) cc_final: 0.7497 (mmt) REVERT: L 123 ASP cc_start: 0.8824 (p0) cc_final: 0.8572 (p0) REVERT: L 220 MET cc_start: 0.8993 (mmt) cc_final: 0.8178 (mpp) REVERT: M 255 MET cc_start: 0.7882 (tpp) cc_final: 0.7565 (tpp) REVERT: N 255 MET cc_start: 0.6226 (OUTLIER) cc_final: 0.5700 (tpt) REVERT: O 166 GLU cc_start: 0.8292 (mp0) cc_final: 0.7954 (mp0) REVERT: O 180 ASN cc_start: 0.8759 (t0) cc_final: 0.8440 (t0) REVERT: P 90 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7435 (tm-30) REVERT: P 255 MET cc_start: 0.5979 (mmt) cc_final: 0.5084 (tpt) REVERT: P 309 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6704 (pp30) REVERT: Q 59 PHE cc_start: 0.8581 (m-80) cc_final: 0.8225 (m-80) REVERT: Q 123 ASP cc_start: 0.8227 (p0) cc_final: 0.7952 (p0) REVERT: Q 255 MET cc_start: 0.7080 (tpp) cc_final: 0.6524 (tpp) REVERT: R 86 GLN cc_start: 0.7398 (tt0) cc_final: 0.7033 (tt0) REVERT: S 152 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8022 (p90) REVERT: S 166 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7311 (mt-10) REVERT: S 219 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7651 (pp20) REVERT: U 100 CYS cc_start: 0.8731 (t) cc_final: 0.8338 (t) REVERT: U 132 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.6340 (ttp-170) REVERT: U 234 PHE cc_start: 0.8970 (t80) cc_final: 0.8646 (t80) outliers start: 125 outliers final: 105 residues processed: 422 average time/residue: 0.4973 time to fit residues: 364.5268 Evaluate side-chains 444 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 326 time to evaluate : 4.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 165 TRP Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 293 MET Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 180 ASN Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 303 VAL Chi-restraints excluded: chain L residue 319 ILE Chi-restraints excluded: chain M residue 30 CYS Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 134 SER Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 163 MET Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain N residue 80 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain N residue 307 ASN Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 30 CYS Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 194 ASP Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 309 GLN Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 62 HIS Chi-restraints excluded: chain Q residue 134 SER Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain Q residue 308 HIS Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 143 ASP Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 152 PHE Chi-restraints excluded: chain S residue 163 MET Chi-restraints excluded: chain S residue 165 TRP Chi-restraints excluded: chain S residue 219 GLU Chi-restraints excluded: chain S residue 220 MET Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain U residue 90 GLU Chi-restraints excluded: chain U residue 97 THR Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 163 MET Chi-restraints excluded: chain U residue 220 MET Chi-restraints excluded: chain U residue 265 TYR Chi-restraints excluded: chain U residue 280 ILE Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 305 HIS Chi-restraints excluded: chain U residue 308 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 332 optimal weight: 6.9990 chunk 445 optimal weight: 0.3980 chunk 128 optimal weight: 0.8980 chunk 385 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 418 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 429 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 180 ASN P 184 HIS ** Q 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.095267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.077956 restraints weight = 97607.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.080762 restraints weight = 54445.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.082673 restraints weight = 36827.056| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 44149 Z= 0.229 Angle : 0.667 47.283 59959 Z= 0.367 Chirality : 0.047 1.571 6290 Planarity : 0.005 0.195 7837 Dihedral : 5.638 87.374 5901 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.35 % Favored : 93.61 % Rotamer: Outliers : 2.55 % Allowed : 15.21 % Favored : 82.24 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.11), residues: 5355 helix: -0.43 (0.13), residues: 1564 sheet: -0.01 (0.15), residues: 1173 loop : -1.61 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 165 HIS 0.323 0.002 HIS U 285 PHE 0.016 0.001 PHE D 118 TYR 0.021 0.001 TYR J 201 ARG 0.003 0.000 ARG D 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8099.14 seconds wall clock time: 150 minutes 47.16 seconds (9047.16 seconds total)